Honestly, he's only 12 weeks old. He may need some extra rocking or nursing. I don't think cosleeping with you is a problem, unlike other people. He doesn't need to "sleep independently" at 12 weeks old! My kids were rocked and nursed to sleep and eventually learned to sleep on their own - not by being cast out/aside, but by me listening to their cues and doing what they needed, as it sounds like you're doing now.
I strongly recommend "Happiest Baby on the Block" by Dr. Harvey Karp. It is in book AND DVD form! You can watch the DVD during those late nights! He advocates the 5 S's: swaddling (are you swaddling??? It is wonderful for these fresh-out-of-the-wombers.),side, shushing, swinging, and sucking (nursing or paci). He also talks about the "4th trimester" as babies get used to "our" world outside the womb. He's wonderful. You HAVE to read his book or watch the DVD!!! Here is his website: http://www.thehappiestbaby.com/ You can actually get some info there, too. But if you only have 1 book to read on infant development and sleep, this is the only one I would recommend!!! He is so understanding of how babies are!
****ETA: Please please please do not add cereal to his bottle. Don't let anyone tell you to do this. Except for babies with reflux, any pedi worth his/her salt will tell you cereal should only be fed off a spoon! Cereal should be held off as long as possible. The AAP recommends exclusive breastfeeding for the first 6 months, though pedis will tell you it's ok at 4. Cereal in a bottle is a huge no-no (i don't understand why people persist in spreading this myth) and much research shows that solids don't really help a baby sleep longer at night anyway. Breastfed babies are also different than formula-fed - growth charts and "normal" are based mostly on formula-fed infants and can be confusing if you're dealing with an EBF baby.
Also, a poster mentioned a growth spurt....My pregnant brain forgot about that possibility! Babies go through growth spurts at 3, 6, and 9 weeks, and 3, 6, and 9 months. Through this time, they need to nurse on demand to make your supply meet their needs. He may be telling you he needs to nurse more!!!
I also agree that CIO is not a good option at this age. I personally don't think CIO is a good option any time, but that's for each individual to decide for her family. However, many pedis will tell you don't think about CIO until 6 months or more. 12 weeks is definitely too young for that!
I really do recommend Dr. karp's book - it will give you lots of insight on your little man and how he operates!