I would say the Armada game is #1.
WFC/FOC is the better cinematic experience, but the Armada game had 3 playable characters, each one with a completely different feel to how they move and handle, giving you a completely different playing experience based on who you were playing as. The vast number of minicons gave you plenty of combat options to mix things up with (wfc has the standard stuff. Grenades, sniper, machine gun etc.) Armada has these, but it also has things like combat shields that hurt people when you plow into them, tractor beams so you can grab people, spin them around you cowboy style and fling them off the top of waterfalls/cliffs, and tornados. You CAN SHOOT TORNADOS AT PEOPLE!!!
Finally, Armada has some insane enemy AI. I've never actually seen AI like it before or since. The enemy works together to trap you. They coordinate their attacks if a commander is present. If you take out most of a squad, one of them will run off to get reinforcements from another squad if one's nearby. Each enemy unit is it's own threat with it's own stratagies. It's not a cass of the bigger guys just being more guns and more HP, there's actual stratagy involved in taking them all down. Transformation is super quick, and the flip you do let's you use it well in combat, something no other tf game has achieved due to them always taking ages to transform. And it has this moment:https://www.youtube.com/watch?v=k52JxSxE4Ug
I had no idea Tidal Wave existed as a character when I played this game, so that moment was just jaw dropping, pant shattering to me.
The WFC games are a better storyline, better acting, better movie. But I find the aethestics of the enemies blend into the backgrounds making them hard to see. The weapon varieties are not as good, each character feels the same to play (except for Grimlock and Bruticus).
And I would rank WFC as better than FOC. The way it has a dedicated Decepticon and Autobot campaign that blends the two together rather than the one single style. Don't get me wrong, the WFC games are amazing and well worth playing, but my top three would be:
1)PS2 Armada Transformers