Yeah, barring Xenoblade and possibly XCX, Gears and Saga were filled with several sympathetic antagonists as opposed to right out evil villains.

The Masked Bishop and the Godwins from Suikoden are also pretty sympathetic once you really start to learn about their motives.

Myria in Breath of Fire 3 is a nice shout out as well, especially amusing when she was basically chaotic evil in BoF1 and implied to not have changed much in BoF2's backstory. In fact starting with BoFIII most of the games have had sympathetic antagonists more than villains.