Since this is by far the biggest TF comic universe by far (the 125th issue was like waaay long ago now) they have (for the most part) done a fantastic job of intertwining it all. Which sadly for you makes picking particular issues to read to be up with plots that have contributed to what is happening now rather hard.

However if you want to read some of the best comic series they have done I heartily recommend the following series: All Hail Megatron, Last Stand of the Wreckers, Autocracy and as many of the Spotlight's as you can get your hands on Also the early ones with the Thunderwing arc are very good