Yeah, it's not just the loading. There's a noticeable delay between choosing the command and it actually happening.
That's not a technical issue, it's part of the battle system. FF5 and 6 had the same delay, it's meant to approximate a turn-based system where you have to think ahead a bit and perhaps queue spells in advance, etc. The difference is that in FF9, the animations are longer, and since (as in all FFs before X-2) only one animation can play at a time, any spells set to go off during an animation won't actually go off until it's over. So although the delay feature itself is exactly the same in 5, 6, and 9, it might feel different in 9 than the others because of how it interacts with other aspects of the battle system and presentation.
Personally, I still like the delay; setting up spells to go off at just the right time adds a bit more strategy and tension (my favorite battle was vs. Trance Kuja where you had to anticipate when his Reflect would wear off, and time your own Reflects to keep yourself covered). Can't stand the load times though.
