Personally, I loved the EGA QFG2 the most. It strangely felt like it offered the most freedom while it was clearly the most constrained due to the timer - I never felt like I was pressured by the time to choose activities or miss things I really wanted to do. The text parser opened quite a few possibilities - one of my favorites is that, as a Fighter with added Magic, I could "DROP SHIELD" before any combat and use my magic freely. I think it was the only game in the series to have a unique Fighter-only "quest" (really just one event, but name any Fighter-related thing in any other game that isn't also available to the Paladin), which made the Fighter feel a bit less like an excuse to make the player fight more monsters. The combat was one of the best implementations in the series, I thought - granted, I'm not sure there was any difference between blocking or dodging in specific directions, but the high/low swings definitely mattered at times, and magic was much less of a chore to use than the later "click the magic menu, hit the spell you want, and click back to combat so you can dod- oops, you're dead" systems. QFG4 had good combat as well, and was a great game in most respects, but there were a few bugs that made it into the final product that really soured my opinion of it (and I hated the way it automatically gave Paladins a Magic skill halfway through). The VGA remake of 2 seemed okay for a while, but I got into a random battle in an alley when I hadn't saved in a while and never felt like playing it again.
As for 3 and 5... almost the opposite of 2 to me. They're so story-driven that no matter how much you explore, it never feels like the story is letting go of you. I thought 3 was pretty dull overall, and 5 reeked of the multiplayer aspect they never implemented.