Did you even vote in the poll?
No. At the time, I was too busy with my own polls:
Anyway, for me there were two issues that made JA2 not quite being the awesomest game of all time:
1. Rather boring encounter design. But I guess that's the price you pay for having a realistic setting. X-Com was more exciting in this area. Although it does have a thinly disguised Cleve Blakemore.
There are melee attacks, ranged attacks, super long-ranged attacks, burst attacks, AoE attacks, rooftop attacks, crepitus attacks, bloodcat attacks, tanks, alarms, destructibility, tactical detonations etc. There is stealth and camo. There is also phased encounter design, which ToEE has as well. For example, you can injure someone and dialogue pops up that allows them to be reasoned with/surrender/hand something over.
Yes, we mostly go up against humans. As you say, it's realistic unless we go sci-fi mode for crepitus (of which there are a few kinds). But each human can do much more than just attack. They can pick up and use items in the gameworld. Also, consider their movement and stances: each enemy can walk, run, climb, duckwalk, army crawl, strafe, backpedal, swim and vault over fencelines. This leaves other RPGs in the dust.
2. Hard to find the optimal version to play on a modern computer.
Straciatella doesn't have the same options when it comes to screen resolution as 1.13 does, but 1.13 Vanilla is severely bugged. And there seems to be no concensus what is the up to date version of the full 1.13.
1.13 is not the official Sir-Tech game, though. It's a mod. So is Strac. The official 1.12 version is rocksolid, and runs under Strac reliably.