In my own experience, M16A3's undergoing heavy firing (defined, in my case, to be a rate of fire that melts the handguard and/or destroys the gas tube) don't choke on the carbon or heat. The weapon is still operating properly at the point where one can no longer hold it without gloves. Once it cools down, though -- well, that is a different story. I don't see a piston helping with that sort of heat however. The barrel is often trashed after this and the operating system won't fix that.
As for the cleaning issue, I will accept that. I've never had to clean a piston AR but I can't imagine it being any dirtier than a DI. It's not that bad, though; my preferred method is to scrape the worst of the carbon off with a stripper clip, soak everything down well with oil or solvent, and start scrubbing. There are only a few spots where the carbon really builds up and even then, it's not that big of a deal.
It's worth repeating that the gas piston (and direct impingement, for that matter, which was ~50 years old when Stoner considered it) are not new solutions to anything. They're merely different roads leading to the same destination. For the M16/AR-15, and what it's meant to do, it's my belief that DI is just fine. For something else, other rules apply.
Let us return to the OP's question: assuming an equal build quality, are there any disadvantages to a piston upper from a purely theoretical standpoint? I submit the following:
1. Unnecessary complication.
2. Added weight.
3. Increased/altered recoil impulse.
4. Increased parts count.
5. Fouling concerns with gas system.*
6. Cleaning concerns with gas system. **
* You know and I know that a properly designed and manufactured gas cylinder and piston are essentially self-cleaning; however, consider every time that someone has posted on here or somewhere else about how their gas piston isn't moving freely under gravity due to fouling and such, and think about how many DI AR users have complained that their gas tube was blocked. There's something to be said for the AR's gas tube in this regard.
** Clean rightside-up if the gas system is on top and upside-down if it's underneath, right? So says the manual, because we don't want solvents and oil getting in there and dieseling or coking later. Now, it's theoretically possible that the same thing can happen in a DI but really, does it?
There are probably some things that I'm missing. More additions are welcomed. Let's answer the OP's question.