I prefer 2e.
My #1 reason is familiarity. 2e is very similar to other d20-based games, so it's easier for my players to adapt. "If you've played Pathfinder or D&D 3.5," I tell them, "then this is almost the same." Instead of explaining to them how the mechanic works, I can just highlight the major differences (e.g. Toughness Saves, no AOOs) and move on.
In contrast, 3e is very different from other d20-based games, so it takes players longer to get the hang of it.
As an aside, they made a lot of pointless changes (IMO) in 3e. I suspect most of this was just to distance the system from D&D, Pathfinder, etc. For example, "feats" became "advantages," but they work almost exactly the same. So why change the name? Another example is ability scores, which went from 6 to 8, and changed from a more familiar 3-18+ scale to a -5 to +5 scale. If you're new to roleplaying, it's po-TAY-to vs. po-TAH-to, but if you're coming from any other mainstream d20 game, it takes some getting used to (needlessly).
I do like how M&M 3e handles powers better than 2e, especially when it comes to designing Devices and Equipment. But 2e isn't bad enough to make me want to upgrade to 3e.
2e also has a better selection of sourcebooks. In 3e it feels like they went to a lot more online content (Threat Reports), which, to be frank, feels like they're nickel & diming me. I'd rather pick up one sourcebook with a wide range of new rules, characters, and info, than a bunch of piecemeal PDFs. Also, I like having books on the table, rather than have to look things up on my laptop. You can find almost all of the 2e sourcebooks on Amazon or eBay for reasonable prices.
While on the subject of sourcebooks, I really like Freedom City, and they don't have a version for 3e. I've not looked at Emerald City (the 3e city sourcebook) yet, but I've heard from the reviews that it's junk. Besides, the only copy I could find on Amazon was $60, which is way too much.
I do wish 2e had an online reference document, like 3e does. But again, it's not enough to make me want to upgrade to 3e.
I kind of hope they come out with a 4e that goes back to the d20 roots, but combines it with the better power rules from 3e. That would be enough to get me to upgrade.
Hope this helps.