I don't think the more I play will change my opinions really. My comparison isn't based on how well i play, but on the games themselves.
BF3: Time played - 4 hours MW3 12 hours
(The pros and cons were easier to do based on BF3, and not both....to keep it relativity short)
Graphics/maps
Pros
Lighting is almost perfect. As are shadows. Textures are clean and crisp in all parts of the maps. The graphic realism is much better then MW3.....but the difference when it comes to game play is nominal.
Maps are all well made. Mostly large maps. The best thing I have found is the map interaction. Unlike CoD, almost every map element is able to be interacted with. You can blow holes through walls, destroy bridges, take out trees, ect. There are some map elements that can not be altered, but for the most part the map at the beginning of the match can end up looking almost completely different then at the end.
Maps do not typically have a "defined" edge by being blocked off. You will receive a warning when you cross a line "outside of the map". But not having a set boundary seems to mentally extend the map sizes farther, giving them even a larger, more realistic, feel then they actually have.
Choice of spawn points in some game types including spawning near "friends" and at times, inside vehicles
Many indicators of where your team is and your teams vehicles. It is easy to group up and stay together in almost every map. Also easy to see if your team is concentrating on a specific area so you can get there to help fairly fast.
Cons:
Finding the enemy in large maps can take longer, sometimes making for slower game play at times.
Having the ability to destroy portions/walls in the map, you are sometimes limited when trying to take cover. Although that makes it more realistic, it can be frustrating at times when you have people randomly shooting with tanks, not knowing where you are, bring you out into the open while you are trying to be tactical.
Choosing a spawn point that is "under attack" in some game types can cause spawn frags often. Quite a few occasions I would not even be alive long enough to see where I am.
Enemy indicators are hard to see at times. The CoD top left corner map system seems easier to use then the bottom left map system in BF3. Especially with the UAV/Advanced UAV perks that assist the team on enemy locations.
Although the lighting is realistic, to an extent the reflections and "blinding lighting" is a bit over done. Even though it is realistic to lose a jet in the sun, the amount of time is over compensated for. Too much emphasis on the realistic lighting for a video game. The laser sight blinding is a realistic concept and a nice addition....but the application is really unrealistic. The chances of a small laser blinding you from across the map is slim to none. The laser would have to be in a area smaller then 1 inch to be effective, yet it seems as long as its "close" to you, you get blinded.
There is a graphic glitch that you can prone yourself into a wall partly. Only leaving your head and chest visible making you a smaller target. I saw that at least 10 times or more in every game. That is a major issue that needs to be fixed. Also, you can see weapons glitch through walls. I killed/was killed many times due to "knowing" someones location through a wall.
Game Play:
Pros:
Weapons have a better sound and more realistic feel. Ambient sound is better as well.
The ability to level up and alter weapons as you progress.
No real such thing as "noob tubers" in any match. Rocket launchers in BF3 as essential weapons needed in every map, where as MW3 they become a complete annoyance in most maps.
Realistic bullet trajectory. You must get a feel for distance shooting or you don't stand a chance of hitting anything.
Team help is important. You can be healed, have ammo refills, and repair vehicles on the go.
Class changes are easy and can do after each death.
The ability to use multiple vehicles in almost every map, and a huge variety. Many vehicles are used best with more then 1 person, and there are also transport vehicles to help bring your team to the action.
The action is more intense. Although the map size may make for less action at times, the action you do see is much more intense. Many more variables and many more large scale fights....making for great battles.
Cons:
No real "kill streaks". Although it is nice to be able to use vehicles with out kill streaks, there are some people who camp the vehicles, limiting the time others can use them. It isn't as rewarding personally to have a large KDR, where MW3 awards you the better you do. Although in real life there's no "perks".... having incentive gives personal goals that to me, add to the game.
Vehicles are not easy to master. This is not really a "con" per-say....but it can get frustrating at times trying to fly a jet/copter and finding yourself on the ground faster then you took off. Although again, maybe realistic, I think the game should offer "flight training" offline to be able to better learn air vehicles.
My biggest "con". Unrealistic kills. This can go either way for each game, because they both have issues. I don't think it is something that can ever be "perfected".... but I found more unrealistic kills on BF3 then MW3. Examples: Knowing a guy was in a hallway, I prone crawled to the door. He did not see me at all, I fired a rocket directly into him....he was hit, turned, show 3 shots and I was dead. He was not. I hit about 5 people with direct rockets, 1 died. Grenades seem to have more power then RPG's at times. Example 2: Saw a enemies knee glitch through a wall, prowned to him, shot hit knee clearly in the open, got 3 hit markers...he stood up, came from behind the wall and I shot 2 into his chest. All acknowledged with hit markers...he shot 2 times and (I assume) was awarded the head shot. Example 3: Happened on a few occasions, while sniping....got a bead on someone and shot 3-5 times with hit markers, no kill. Although it seems that if that is the game play across the board, it is still a level playing field to an extent.
Leveling is slow and the results of leveling are not as awarding. Weapon upgrades are existent, but less extensive. You don't have the same feel of "creating" a character as much as just adding to a predetermined class. The customization in BF3 pales in comparison to CoD in general. CoD seems more aimed at the abilities to "create"
Limited game styles. CoD has seemed to put less effort into the maps then BF3, but BF3 has limited game types in comparison. Although the styles they do offer are well thought out, the lack of variety is disappointing.
Many more snipers in BF3 then MW3. Although there is no "camping" really. Snipers are a large and needed class in the game, so the is't not as large of an issue then in MW3
All in all..... it isn't really possible to compare the 2 games head-to-head. Although they may be in the same genre, they are completely different games in almost every aspect. CoD is more aimed for the "new" gamer as BF3 is geared more to the skilled players. CoD is more set as a solo/close quartered game as BF3 is a team based/large map game. It is easier to get frustrated in BF3 due to team dependence where in CoD you can have great games and still lose almost every time.
I enjoy both, but prefer MW3 as far as game play. Even though the maps pale in comparison, they are easier to learn and master. The limited size creates more of a "run and gun" style that is non stop action. However, if you are more tactical minded, BF3 is superior by far. BF3 is more thought based and MW3 is more spray and pray at times.
I think the customizable portion of MW3 is infinitly above BF3, the battle logs page adds quite a bit. It seems the same idea as CoD's Elite service, but is free...also is available with PC, as where Elite is not.
I will continue to play and enjoy both, but know that the mind set prior to picking which to play is different. Both games have their pro's and cons, but both are well made an exceptional games. The differences or lacking of each is made up with the other.
Just comes down to picking. I don't think you can go wrong either way.