Personally I find mass effect far better than Fallout. I should point out I have only played Fallout 3 GotY, while I have played both mass effects.
Warning, wall of text incoming, as well as spoilers.
While Fallout has a stupidly big world, and dispute having an overarching plot it cant be described a linear in any way. I spent literally days roaming around ignore the main quest line to find all the travel points and off plots.
Unfortunately in Fallout at no point did I actually "care" about any of the other characters which loses a lot of depth, and on the one occasion I did take an ally out with me (the big mutant guy) he pulled everything within a 30 mile radius and damn near got me killed.
The scaling is terrible, especially if you have the game of the year version. By the time I got to level 20 the only opponents of even minor consequence were the super mutant overlords, and after hitting level 30 (having wasted 3 or 4 levels worth of perks on pointless things) I had managed to trivialize even them. Leaving nothing within the game that could actually challenge me, and that includes the expansion which lets you get to 30.
The variation on combat is nonesistant. And while dropping a grenade in someone pants was funny the first few times, by the 100th it was waring somewhat thin. Besides, after I found the stealth suit from the outcast brothers, I could literally walk upto any enemy and stare them in the eye and they didnt see me. Meaning I could pick and chose my fights and just burn down big enemies with repetitive pocket grenade's rather than risk an open fight. While I dont object to becoming somewhat overpowered never the end of games like this, I wasn't even 1/4 of the way through by the time I found that suit.
The moral choice system is...To put it bluntly pointless. If you chose to be bad certain plot quests have you effectively wipe everyone out removing half of the side quests with them, but other than that does just about nothing except change what you hear on the radio and who shoots at you. Which in turn results in the mass genocide of 1/2 the population of the fallout world and yet more quests lost. Effectively removing true evil as a moral choice.
And while the terrain looks very nice and gives a very nice atmosphere in never changes. EVER. The only time its not desert brown and concrete gray is when you go into hippy village in the north which lasts the whole of 30 mins and after a while it becomes very monotonous.
Compare this to Mass Effect.
I cared and wanted to find out about the various characters in both 1 and 2. Doing my best to keep everyone happy, while also trying to stay within the strictures of my RP of the mission over everything personality type.
The combat while repetitive never really got old for me. Because while you were essentially repeating it was far more interactive, ducking from cover, angleing abilities to hit people round boxes. By the time I had become an veritable tank as a solider (which is far worse on 1 than 2 if you spend the credits on the armor) I was having small legions thrown at me in ME1, and despite being able to drop most opponents in relatively short order on ME2 if I simply ran at my enemy Id have been cut to bits.
Allies actually have a use, and while on ME1 their controls are clumsy at best, the AI pretty poor and the fact I sent them both on a valiant charge to their doom's on several occasions just to get them out on my line of fire. Both their control's and AI have been greatly improved in ME2, and at no point did they feel a hindrance and on the harder difficulties at least I feel that need to micro manage will possibly become necessary.
The plot had me gripped from start to finish in both games, even having played them out of order (ME2 first).
The inventory system is terrible on ME1 but again like the AI, the dev's listened and its all been scrapped in number 2. Though I grant you having to omnigel the first decent omnitool I got because my inventory was full, nearly had me reloading to last save, the lack of a method to swap out inventory items for the new stuff baffled me, as well as having to omnigel one item at a time, which at its worst when I literally had to empty 148 items from my inventory was nothing short of suicidally depressing.
For all the complains about the mako missions I didnt find them "too" bad. Though the introduction of the planet scanning in ME2 was the games only true Achilles heel, and until you get the mining ship upgrade from Miranda is nearly as depressing as the inventory from the first game. Thankfully on your second run through of ME2 you get a long service bonus of 50k of each mineral which makes replays bearable in this regard, as you can be far more sparing in your scanning and only take the biggest of deposits greatly increasing the speed at which scanning can be achieved.
The moral choice system I think is both one of the games biggest achievement and downfalls.
I LOVE the fact that choices I made in the first game have impacts on the second. And Ive now got 3 games on the run from ME1 to explore the possibilities of the plot lines both at the end of ME1 and into ME2.
Having said that, many options in the game are reliant on you having X amount of moral points. Which leave you, to coin a phrase from Zero punctuation, picking the option that give you the most dick head points, rather than what you actually want to do. My first ME2 character suffered heavily from this, due to the fact I prioritised the mission over everything, and made the choice that "the" mission was the main quest line, placing all other quest as secondard. To give an example, my greatest chance of accomplishing the mission was to have all of my crew loyal to me. For Tali this means stacking up the paragon point, while for Zaeed it actually had me abandoning the original mission in order to complete HIS mission to get him loyal lining up the renegade points. This left me happily out of karmas way by the end of the game, but had lost me several potentially interesting points I couldnt follow in conversations as I had insufficent maral points.
Lastly the boss fights. I had 2 major complainsts. These both come back to the Fallout issue of being overpowered. The first time I fought seran on ME1 I had full sniper spec and an insane 330 damage rifle with that ammo that increases damage by 500% but overloads the weapon in 1 shot. I got this out, used the sniper skill to boost the next shot by 225% fired and hit 1 shot, got my rifle out and before Id managed to get it to half temperature he was dead. Yes I realise I might have been abusing game mechanics JUST a little bit......If fairness however the 2nd and 3rd Seran fights were much more difficult if not exactly taxing.
The same is pretty much true on ME2 with the reaper fight. I got my nuke gun out, hit it in the head and did 3/4 of its health in a single shot. I actually found the freeing it bit more difficult after that.
Finally.
Despite being sucked into both games. I found Fallout started losing me about 1/2 through and while I enjoyed the time I spent with it I couldnt play it again, and I doubt I could be convinced to buy number 4, should it ever be bad unless someone convinces be they have had a revelation in either the story section to make the copy paste terrain bearable, or in the combat department so fighting in said copy paste terrain was more diverse.
Mass effect on the other had Ive completed both once, have 3 more characters underway and the day I find out number 3 is out Ill be reordering it. The story is first rate, and your crew is interesting to the point of obsession (every time I came back to the ship I was back down talking to them to see if I could progress their plots) which both make up for the strictly average combat.
Sorry about that. I think I got carried away. :S