Hehe, this is where things become speculation. In ROTF there were baby Decepticons hatching out of globule pods. But lacking sufficient energon they die. For this Transformers searched the universe looking for Solar Systems that do not support life and would use the Harvester to destroy the Sun in that system to extract the energon needed to survive. Even the Primes did this, which is why they created the Harvester and made it so it could only be activated with the Matrix of Leadership. So if they are having babies coming out of eggs who is laying these eggs? We didn't see a Queen, we only saw a former "Prime" now called the Fallen. But that doesn't mean he's the one having these babies. Maybe he has a mate we are not shown and this "mate" is only used as a breeder and really has no rank and is kept enslaved. Decepticon's are considered evil.
Now if Transformers are able to reproduce, why was it so important for Megatron to get his hands on the "All Spark" that crashed onto Earth thousands of years ago? He should have been focusing on gathering energy as the classic Megatron was obsessed with. What was so important about the All Spark? It turns human technology into evil Robots, revives and repairs Decepticons as well. But whats so special about earth's machinery? Our manufactured machines are not made to last and the materials are shotty.
As for the "brother" analogies; when Optimus called Megatron his brother in the first movie. He could have meant it like a man who would call any other man his brother through mankind. Like a Christian would call any other Christian a brother. Since we are all humans and we must have all descended from some common ancestry we are all brothers and sisters. So all Transformers from Cybertron are brothers through a common ancestor or origin. They may have been created by the same source. Now they can be referred as brethren but not necessarily through blood or birth; But through a common creating process.
If Prime is descended through a Dynasty of Primes, maybe Michael Bay is pushing a birth like creation process through the line of "Primus"? Primus being the first and their God. Prime should be a "King" or a "Pharaoh /Living God" to all transformers. The linage he descends from may have been worshiped or who once rightfully ruled Cybertron in the earliest times.
The Primes were believed to be like Gods or like "Primus". Thats why the Primes and Fallen had those Egyptian Pharaoh headdresses. It is a headdress wore by an Egyptian Pharaoh who was considered a living God on Earth. If Megatron wanted to be a Prime in the Prequel, then that means he is jealous of the lineage Optimus Prime descends from. Megatron wants to be a God/King too. He wants the glory on Cybertron. Even so Prime doesn't even say he is the rightful ruler of Cybertron, and does not wear a Pharoah's headdress. But his protoform may have at one time! Techinically he should be since he is the last Prime. Megatron wanted to be a Prime too. The name "Prime" must literally mean a living God or Pharoah to Cybertronians. Prime however is very humble and has never said this to even the Autobots. But Megatron knows who he really is and hates him. Anyhow Prime considers himself just a transformer like all the others so he will call them all brothers. But of course this is still speculation.
Hehe... So transformers can do this and that and that too? 
[ Click to attempt signal recovery... ]
