Would it be better when opportunity arise to get the original base game or to wait it out for FFG to release a new one ?
Depends on the price (per oshfarms above). If it's reasonable, buy it now. It will probably come with more stuff than any FFG reprint.
Would it be possible that the new release by FFG be somewhat incompatible in some way or another with the base game?
I doubt it would be incompatible in any way, so I wouldn't worry about that at all (if you'd rather wait for FFG).
One thought thats been on my mind since this whole issue arise is that does FFG plan to re release the base set but with less component e.g miniatures and more post-buy work e.g sticking on the flags
Probably yes: less components and more labor (based on FFG's expansion releases).
Are they going to release faction set like horrible hordes ? If they do so how are new players going to get the board?
I believe they will release more "faction" expansions. But at some point they will have to make the core components (incl. board) available again. This I think is the big challenge for them. How to package and market this without a) alienating fans, and b) taking it in the shorts (which is not really fair to expect them to do).