At least you know you can shoot something in ME when it's in the middle of your crosshair, totally not possible in AP. The shot always goes to the very edge of the reticle, which is also far bigger than in ME. Making the pistol totally useless. The special shot where you need to aim for several seconds is also pretty useless since it takes so much time and usually the target moves, which makes it much harder as well.
Thing is it's a stealth game. If you miss something you're fucked (well not in AP since you can basically run through the level and kill everyone like Rambo with ease)
I already know that Mass Effect wasn't that good as a third person shooter (still easily beats AP), but in return it was a much better RPG.

I gave up early on the stealth mechanics since they're not working in 75% of all cases and played the whole game with an Assault Rifle since it's the only effective weapon and it's relatively easy to hit someone (still a pain).

Skills in Mass Effect are far superior and actually useful
http://rorshock520.files.wordpress.com/2010/07/mass_pt1_stats.jpg
At least 9/13 of them make sense, but in Alpha Protocol only Toughness and Martial Arts are decent. The rest aren't even worth it to upgrade, since you almost don't notice them anyway.

Also the shop in AP is horrible. In the whole game I found 2 guns worth buying and 1 suit and even those had only minor differences in stats.

I'll ask again, 360 or PC? If you played on 360 and they didn't program the auto-aim properly than that will most certainly ruin the experience and the PC version did review better than the 360 version.

You kinda contradict yourself when you say it wasn't worth it lvling up anything but toughness and martial arts, and then saying you couldn't hit anything. My 3 main stats were pistol, rifle and stealth and found the reticle for special shot sped up greatly and general aim was fantastic by the end. I was head-shotting nearly everyone without being seen towards the last levels. I also found the invisibility skill very useful to the point I was using it in boss fights. The skills I found no more or less useful than in Mass Effect.

Also, the shooting mechanic being harder than Mass Effect doesn't make it any worse. I played through all of Mass Effect using only the assault rifle and switching sniper rifle every so often. At least in Alpha protocol I switch styles from all out gunning, to stealthy head shots etc. Point is, you could play it from multiple playstyles. You could play it stealthy, but you could also go in guns blazing, or set up traps or enter from multiple points.

I agree the shop was utterely useless though.

There is no auto aim. And even if there was I would turn it off like I do it in all my console FPS.

I DID upgrade my Assault Rifle skill to 100% and the difference was just so minor that it wasn't really worth it, thus making toughness (for health) and martial arts (for more melee damage and hit combos, since everybody runs towards you and wants to beat the crap out of you.) the 2 only worthwhile skills.
In Mass Effect the skills have a much greater impact. They actually improve something by more than 10%....

And yes not being able to hit something that is in the middle of your incredibly large reticle IS making shooting worse than in ME.

I also stay with my opinion that the stealth system is broken. Go play Splinter Cell or Metal Gear Solid where it's actually possible and rather easy to finish whole levels without being detected once.
There is a reason why only 6% (300 out of 5000) of all 360 gamers completed this achievement:
http://www.trueachievements.com/a62336/one-with-the-shadows-achievement.htm

Unfortunately, no

Skyrim is depicted as northern style snow and ice type region. Being this, I don't expect to see much activity bug wise considering cold environmental conditions seemed to have a negative correlation with insect evolution. Therefore, I expect to see large quantities of bugs in say, Black Marsh which is basically the swamp from which Argonians originated. ES5 though? Not a chance.