Well, honestly, SC already looks to have a major upper hand on this game from a gunplay/stealth/polish/production values perspective SC won't, however, have a non-Tom Clancy storyline written by the Obs staff, nor will it have AP's (hopefully) awesome choice & consequence.
It's really too bad, with the games being released in a narrow timeframe, since AP will get an unfavorable comparison next to SC in those areas. However, they chose to make the actual gameplay action/stealth-oriented, so they either need to up their game or take the flak for it. Unfortunately, I have a feeling the game will be treated as the poor man's action/stealth game. It needs to expand beyond that and offer lots more tactical options, starting with lots of wacky gadgets. Lockpicking/hacking minigames doesn't inspire much, either. I don't think the game deserves a free pass 'because' it's an RPG, and should be called out for having substandard gameplay if that's what it ends up having. Then again, that's exactly what Mass Effect managed, and people are excited about ME2, so we'll see how people receive AP.
Obs needs to show off the RPG/C&C elements more, otherwise they WILL draw negative comparisons to SC, or other weird ones I've heard, like Uncharted 2 and Call of Duty and Gears of War :/ Show more dialogue, more character interaction, more branching C&C, more warring factors. Stop showing Thornton sneaking around in his silly crouching animation and shooting things and playing minigames.