I've long suggested the government is not likely to outright tax Roth IRAs. That would be egregious and ballsy. Also, unprecedented (to my understanding). I suspect it will be more sinister like social security. Initially, social security was tax-free. Then they added means testing to tax a portion of it. You know, if you're wealthy and are withdrawing $20k from your 401k every year in retirement, then you can afford to pay taxes on your social security. The government can then double-down on their dirty tricks and do things like set the means testing not be adjusted for inflation. So every year, more and more people gradually get dinged by it. Like AMT.
The way I suspect this will look for Roth IRAs is:
1) Means testing such that Roth IRAs are tax-free, provided you have under a certain income. "Roth IRAs were never meant to be tax havens for the ultra wealthy 1%ers. They were meant for the everyday common man, scraping together a little here and there for the future. If someone has over $100k in their IRA, they got there through unfair means and we need to level the playing field for the middle class worker."
2) Federal VAT. While Roth IRAs are income tax free, if we change the tax system in the US such that we add a VAT (possibly with the promise of reducing the income tax simultaneously), then the Roth IRA remains untaxed at the income level, but with a 20% VAT, it means you can only use the money to buy <80% less things.
3) Means testing for social security such that if you have a certain level of money in your aggregate IRAs, you aren't eligible for social security or it's phased down significantly. The calculator for SS could be changed such that if you have nothing in an IRA, you get more than the current level, but if you have an IRA you get less. A fair balance since the people who have large IRAs don't need social security which was meant to help the poor.
I imagine all three of these could come into effect. I see federal VAT not being implemented specifically to target Roth IRAs because I don't think the amount of money in Roth IRAs in the US is large enough to justify this kind of a move. However, I see it as a collateral damage of such a shift. The way I see it occurring is an argument that the wealthy are hiding behind tax shields, paying less taxes* than their secretaries, and we need to change the system to make it fair by adding a VAT so when the fat cat CEOs go to buy a private jet, they pay their fair share of tax. Regular middle class people will be better off under this new fair taxation structure.
*the uber wealthy pay less marginal tax rate than their secretaries, albeit paying 1,000,000x more nominal taxes because their tax base is significantly higher.
With respect to using IRAs as a form of means testing, the obvious answer is "pull out the principal contributions from the Roth IRA, tax-free, principal free if you're under 59.5, immediately, so you don't get caught in that means test. Or, if you're older than 59.5, take the whole thing out tax-free. The problem with this strategy is if the government is specifically making a new system to screw over people with Roth IRAs (or large IRAs/401ks in general), then the legislation will include a look back period, retroactively.
Such that, if you had an IRA with a balance of above $X at any time in the last 5 years, then that's used by the means testing.
Given that as a possible parameter, how can be avoid that? First, let's identify the political framework for which such legislation might be passed, and begin considering pulling out IRA money before things get proposed officially. As an example, if you're in Venezuela and the government is talking about seizing private bank accounts, it's already too late. But if you notice the government is corrupt and broke, and seizing private bank accounts is all that's left, then it's time to consider action in advance while there's still time.
What might this look like in the US re: new IRA laws?
a) Democratic control of congress and executive branch; in the current iteration of republicans, this won't pass
b) Another political movement like Occupy Wallstreet where people are brainwashed into hating "wealthy" people
c) A growing divide between the rich and the poor. It's growing as we speak, and the bigger it gets, the greater risk of IRA changes
d) Talks about imminent insolvency of social security and a need to reform the system
These are the canaries. If they start dying, it may be time to cash out your IRA for gold coins and go on a boat trip.
Further, consider how the government would impose such IRA means testing restrictions. They would need to know how much every American has in their IRA every year. Currently, while the government certainly has access to that data, I don't believe it's in an easy-to-read aggregated location for the IRS/CMS/SSA to access. In order to do means testing, the government would need to have Americans file a new form with their taxes each year, for the total amount of their IRA/401k holdings. Custodians would be required to submit paperwork to each taxpayer and a copy to the government, like 1099s are today.
The government may be stupid, but not when it comes to stealing money and in that respect, they are insidious. Don't think "they" will propose IRA means testing legislation with a retroactive backdating period, and not have already been collecting this IRA balance information for several years, to ensure their backtesting can maximize tax revenue.
What this means is when the government is considering this type of IRA Means Testing (either for additional taxation or reduction/elimination of SS benefits), they will come up with an excuse to force Americans to start filing IRA balances on their tax returns for several years leading up to the point where the new anti-IRA legislation is even discussed publicly. Perhaps it will be to combat terrorism or child pornography, since IRAs are where those two criminal groups hide their assets. Or, perhaps it will be to ensure Americans receive their IRA distributions tax-free, as promised, without question. Regardless of how they frame it, once declaring your annual 401k/IRA balances becomes part of mandatory tax filings, that's your biggest canary to bail out.
The second biggest canary is having similar, weaker legislation proposed. The government is keen on testing the waters to see what they can get away with. Like going to war with Syria. It's a lot like a teenage boy having a "random" discussion about another kid from school who's parents let him get a tattoo and how cool it is. The teen boy is not asking his parents if HE can get a tattoo, he's seeing whether his parents say "tattoos are stupid and that kid's parents should be shot for letting him get one". And if the parents say that, the kid knows to shut his mouth and not even ask. The government pulls this regularly. CISPA was another good one recently.
I don't know what this weaker form of IRA taxation legislation would look like, but as soon as there's any hint of even a dilute form of it being discussed (such as limit IRAs to $1M total), then we're one step closer. Perhaps this $1M annual restriction, will be the stated justification for mandating all Americans file their IRA balances on their tax returns each year. And 99.99% of people won't care because they have well under $1M.
But of course, that $1M won't be pegged for inflation. And it may be discussed in public as $1M, but in the actual legislation there's an asterisk that says $1M per household, $500k per single taxpayer, and all of the sudden the government cut that threshold in half, instantly. Much like Obama is fond of saying he will never propose to raise taxes on people making less than $250k per year, what he means is FAMILIES making $250k per year, or individuals making $125k.
Because clearly, a single male living in San Francisco or Manhattan making $125k/year is uber wealthy living in his fat-cat $2500/month studio apartment with combination toilet/kitchen sink/bathtub.
Another possibility is when more "wealthy" Americans decide to shrug and leave, the government may block people from taking IRA assets out of the country before age 60. You know... to "ensure the appropriate taxes will be paid during retirement and distribution". Or more likely just tax the whole thing if you move out of the country, because (with a traditional IRA/401k), you didn't pay taxes on that money when you got it, you deferred it, and if you leave the country before paying those taxes, you're cheating. And, Roth IRAs will somehow get lumped into that, too. And this may also be justification to mandate annual reporting of IRA/401k assets to government. As well as include restrictions on liquidating/withdrawing IRA/401k accounts, to prevent tax-cheats from leaving the country. Maybe the restriction is only taking out 20% of your total account balance per calendar month. To prevent international escape. With the side benefit of when future IRA taxation is added to every American, the people who decide to clear out their IRAs will be legally unable to due to this restriction.
SUMMARY:
IRA/401k changes are likely to occur in the future because government can never steal enough money from tax payers. Currently, it makes sense to max these accounts out, but as time progresses, and we inch closer to the point of screwing over IRA/401k owners, we will need to develop an exit strategy and it will need to be implemented in advance of legislation, possibly several years in advance. Thus, we need to monitor the political climate for clues that this is going to happen, such as:
1) Democrats in power
2) Discussions of any form of restrictions on IRAs/401ks, for any reason, whether it be maximum lifetime aggregate levels, withdrawal restrictions, or country exit taxes.
3) Mandated reporting to government of IRA/401k balances is another key indicator that imminent legislation to tax these accounts is in the works.
Keep on thinking the government can't do something because it wouldn't be fair. 
