Not sure about anyone else but to me, AP had the allure of a Bourne film or the TV series, 24, going for it at the time. It had to feel like an action film and I think it struck all the right chords with dialogue, storyline and choice. I liked the idea of an RPG set in an espionage setting. I thought it had wider appeal than a space opera or some fantasy epic dungeon crawl.
With some tinkering to the gameplay mechanics (Smarter AI, have weapon skills improve damage instead of accuracy and leave the shooting to the player, level designs to help players better exploit stealth or gadget use), AP would've been a perfectly fine game.
I think SEGA knew what they were funding because it's not like they haven't funded RPG's before that are downright revered now like Skies of Arcadia. They were doing business with the company that made KOTOR2 and that sold like nobody's business despite the rushed deadline.
Ultimately I blame SEGA as a producer. I think if they had better supported the ambition of the AP dev team, this game would've turned out much better.