There are definitely many factors that could change the outcome of the battle. I think that the biggest variable will be the battle stage. The Strike Freedom is a space gundam and thus will preform better in space. Its dragoon system is only capable of operating in space. On the other hand you have megatron who on land would be fast and agile proving to be a worthy opponent of someone like the strike freedom.
The last factor is whether Kira who is the pilot of the freedom can go "seed." If he can then all bets are on freedom no matter what