I look forward to seeing what you come up with! While I've been enjoying the game quite a bit as-is, I admit there are a few areas that could use some refinement. In the interest of not re-inventing the wheel, I thought I woudl point out that there has a been a lot of discussion about this very topic over at the
SG forums. Check out these 2 threads in particular:
http://forum.spartangames.co.uk/smf/index.php?topic=7771.0
http://forum.spartangames.co.uk/smf/index.php?topic=6037.0
I'll also try to briefly summarize for those that don't have time to read through all that

.
While of course there are many different opinions and thoughts on this topic, there seems to be a wide consensus on several particular issues:
-Some models are not pointed/stated well. One example often cited for under-costing is the
PE Sky Fortress, while an example of over-costing would be the KoB battleship.
-Obscured flyers are generally regarded as
OP, due to the resiliency gained by only being hit on a 6; this problem is exacerbated by the Altitude Skimming MAR. A common proposal is to nerf this modifier to a 5+ instead of a 6.
-Some players have expressed concern over Indirect Fire; using an attached recon plane and a scout flyer allows a modification of indirect fire such that it hits on a 4+, like a normal shooting attack would. This would mean that a fleet with long range shooting could sit back behind an island and pound any approaching enemy without reprisal.
-Tiny flyers a bit too fiddly for their own good. Proposed solutions include dropping the fuel tracking entirely, or limiting tiny flyers to only those that can be launched by a carrier (ie, no automatic 10 free tokens).
-As a subset of the point above, Tiny Flyers are also of limited value due to their vulnerability to Ack Ack and the length of time involved in re-arming and re-launching them after they have made their attacks.
-Faction Balance: Right now, there is a lot of debate over which faction is the "weakest." The KoB are commonly discussed here, due to their under-performing cruisers and battleship, while the
PE are also often discussed as being towards the bottom due to their relative fragility (no shields on the cruisers) and lack of a weapon system that is not affected by damage (like bombs and torps). One often proposed solution to that problem is to house-rule that Tesla weapons are not affected by damage. The FSA are generally described as being a bit over the top, as they have a strong defense (shields, an additional point of DR over other factions) and a strong offense (effective long range shooting).
There are probably more points I'm glossing over, but those are the ones that immediately spring to mind!