I don't think Gears of War does the cover system any better at all. It suffers from the exact same 'one button does everything' thing that Mass Effect 3 has, and now that ME3 has a roll, quickjumping over cover instead of having to crouch down into it before you can hop over, grab kills, and going around corners without leaving cover, there's really nothing left that Gears does any better.
Similarly, active reloads are not particularly skill-based and are definitely not interesting at all. Either you do it right (there's only one way to do it right; there's no on-the-fly decision-making, just a really easy 'hit the button at the right time' mechanic) and you get a bonus, or you don't do it right, and you don't get a bonus. The extent to which you have to catastrophically fuck up the timing to actually get the failed reload is such that I don't think it ever happened to me more than a dozen times throughout all three Gears of Wars combined, and it isn't even all that much of a big deal if you do screw it up. It just means that you have to wait another two or three seconds before you can shoot again.
The boss fights are unique, but they're still boring and scripted to all hell. If they didn't have cool visuals to go along with them, mechanically they'd be dull as hell. Both ME3 and Gears of War are only ever really good when they're putting you up against a variety of standard enemies, where all the normal rules apply.
And Gears is just a standard shooter where the choices that let you prepare for combat are basically limited to choosing two out of however many weapons (and further limitations apply there, be they 'hard' limits, where a certain weapon just isn't available for that part of the game, or 'soft' limits, where you can technically keep the weapon, but you'll have a hard time getting enough ammo to actually make proper use of it).
In Mass Effect 3, the preparation options you have range from lasting for an entire playthrough (your class choice) to 'the rest of the playthrough' (which weapons, armour, upgrades, etc you choose to purchase/upgrade, and which skills you choose for yourself and your party members, although there's a limited ability to respec the latter), to 'for the whole mission' (which party members you decide to bring along, which armour you want to wear, which weapons you bring along), down to the moment-to-moment decisions that are common in any shooter, like enemy prioritization, positioning, which weapon to use and how much ammo to save before grabbing a refill, whether to retreat into cover to recharge or whether to poke your head out and keep attacking, etc. Only there are other considerations that are not in a standard shooter like Gears: Which weapons and skills your squadmates use, which skills to use once your cooldown comes up, along with the skills that use non-cooldown resources (those that are limited based on a stock of consumables, like grenades and medi-gel, or on some other resource, like Nova requiring you to spend your Barrier).
The general feel of shooting, moving, and making 'shooter' decisions is about on par (that is to say: It's definitely no Vanquish, but it's certainly not any worse than Gears), only there's an entirely separate dimension to the combat since your longer-term decisions play into which options are available at any given second, and since you have options like Biotics and tech that simply aren't available in a standard shooter. You're also given much more feedback in ME3 than you are in Gears: Your health is an actual goddamn health meter, instead of a vague red screen overlay, and you can see the enemy's health meter as well, instead of just having to plug shots into them until they die. The Shields/Armour/Barrier/Health dynamic is more interesting than enemies simply having an HP bar, and I thought there was a much more interesting variety of enemies in ME3 in comparison to Gears.
Basically I think Mass Effect 3 is easily on par with the biggest 'pure' third-person shooters (Gears, Uncharted, etc) in terms of being a 'pure' shooter, but it goes above and beyond by having the customization aspects and the greatly expanded repertoire of abilities. If you're going to call it a "mediocre" shooter then I think you have to explain which games you're comparing it to. If those games aren't Vanquish or Serious Sam or something, I don't think the argument holds much water.