MegaGlest has a better AI than GAE. So if you want to play a 1 player game and be challenge then MegaGlest is the way to go if not you will get board with GAE AI soon enough.
I would say that's for the most part wrong. GAE has lots of little AI things like auto-return and auto-repair that make your units a bit less zombie-like and more intelligent. I always found GAE to be a lot more fun to play than MegaGlest. Also GAE's pathfinder has always been way less laggy. Plus GAE has specular and normal mapping as well as per-pixel lighting coming soon. Basically, GAE is smoother gameplay, with better graphics.
Maybe you should actually try megaglest 3.5.1 before talking. You sound like you're talking about the first few versions of it.
If we're talking about that, then you're 100% correct. Gratz.
Anyways, Softcoder has improved the AI a lot, and the pathfinder too. GAE hasn't really tried to improved the AI much, ask the developers. Then there's the default resource multipliers, compare MG's to GAE's.
MG=Ultra, 2.0 Mega, 3.0 GAE=Ultra, 3.0 Mega, 5.0 The AI is ultimately much better in MG.
Now graphics wise, of course with the additions of specular and normal mapping, GAE is better that way. Which is awesome. Tileset particles partially make up for that though, sometimes. Just look at Annex.
Pathfinder-wise, I think MG has improved it a bit. It doesn't cause lag anymore. We did a lot of pathfinder-nodes tests.
Autoreturn and repair is great, but just a feature really.
Basically, GAE is smoother gameplay, with better graphics.
I am afraid this is purely your opinion.
Isn't everything? He doesn't need our opinions, he can try both for himself and see. And of course, the best neutral comparison is as Ultifd pointed out: https://docs.megaglest.org/Engines#Comparison_of_the_Engines
Nope, just some things. The comparison is great for general stuff, though.