Wow, this is tough. I've loved editions when they were new, but that doesn't mean I continue to love them, or even want to play them.
It's not 4e. I played a good deal; I've not against it. But it's the one edition I never ran and that's for a reason.
It's not 3.x. I ran 11 years worth of campaigns in that system, starting with a session 0 before all three of the 3ed core books were out, well into 4e times. I completely burnt out on running it and playing it. Hmm, I'd play 3ed or 3.5 again if it was core books only, no splatbook-of-the-month.
It's not AD&D 2nd. Some of my greatest stories and most memorable characters come from the decade of playing this. But that nostalgia is for the group, not the rules. The modern era of RPG design gives better rules with less complexity, and can mimic the feel if wanted.
It's not AD&D -- that's a worse mechanically AD&D 2nd before organizing everything, and without such the weight of nostalgia. I can only name one AD&D character I ran, David of Corad. A magic user who made it up to 5th level when most of the rest of the PCs had died and been replaced multiple times (and all started at 1st). The paladin also survived, and I think we were about to embark on a Holy Beer Run of Saragen.
I started with Moldvay Basic, which is the Red Box, though the only other local person I had to play with had the older blue box that came with cardboard chits instead of dice. Still, levels 1-3 before getting Expert, class and race mushed together into a single choice, I can't say that's my favorite.
If we stick strictly to D&D-brand only, I don't think I have a second favorite. I can't count a system I'd be unwilling to play as a favorite, even if there's nothing but my top favorite above it?
Can we expand out to d20s and other OGL games? Because then D&D 5e gets knocked down to my second favorite and all is good. (And I'm going to break the rules and say that 13th Age would be my favorite in that case.)
EDIT: Fixed typo.