I like the idea of some kind of FI, but I would execute it completely differently. Say, the other way around.
To me, it would be a "Fleet Index", a single number that describes your fleet commonality costs. Your company gets one FI, not one per fleet. You cannot pay to make it go up or down, it's simply an indication of how well organized your fleet choices are.
FI 100 means perfect, basically single fleet. FI 0 means horrible, like a 40 airplane airline operating 12 fleets.
If Sami now does all the work and introduces "intra-type commonality" (and I really hope he does) than this would mean we could finally get away from this static and unrealistic "4 fleets are bad" rule. Commonality costs would be gradual and depending on how close the airplanes are that an airline operates. One airline flying B737classics, B737NG, B757 and B767 could have a higher FI (and thus pay less) than a company running MD80s, A310s and B777, dispite having more types by the old rules. With this new FI rule, we could completely forget counting fleets, you would look at your FI and that would tell you your commonality costs, no matter if you run 2, 3, 4 or 8 fleets.
For airplanes very similar to each other the FI would only take a slight hit. For example DC9s and MD80s in the same airline would only make the FI go down by like 3 points, where as DC9s and B737classics would cause a 12 point hit, or something like that.
The resultant factor could then be multiplied with the total number of aircraft, so that it still has the kind of damping effect on uber-big airlines.
I also really like the idea of "manufacturer sponsored training and/or maintenance". Because overall this kind of FI rule would of course make the big manufacturers only even more attractive. So maybe Sami could introduce this kind of counter measure. If - for example - MD sells only 200 MD80s while Boeing sells 1500+ B737s; MD could offer "Manufacturer sponsored Crew Training" for 5 years, which would give an overall FI boost of 5 points for the given time. Or they offer to maintain your airplanes for you, reducing your costs and also giving you +5 FI points. If some manufacturer gets really desperate, they may even offer both and thus give you a + 10 FI points advantage. That might even get airlines to jump ship and consider types they previously didn't think about.
Of course all of this will help certain airplanes more than others, I think the MD80/90 would see a good boost, the DHC-8/Q400 probably as well. But that's not the main point. For me the main points are:
1.) the FI gets displayed on the Dashboard, once you worked with it for a bit of time it should be easy to understand and not work its magic behind closed doors, like the rules now do.
2.) it would be way closer to real life; and I think the reason most of us joined this game, is because they love real world aviation. So we should strive to emulate it as closely as possible while still preserving good game-play.
I hope all of this was easily understandable

Cheers,
Cedric