You can correct for the transformer magnetising current but it will do nothing for losses. Where you may gain a little bit is in the reduction of alternator loss with the removal of the magnetising current it has to supply.
The main snag is that it is a variable frequency system and correct capacitors to neutralise the magnetising current at cut in will give you a leading power factor load at higher speeds. This may not be a disadvantage as it will increase the alternator excitation. All depends on your load matching this may be an advantage if your high end loading is light but if it is heading to stall in high winds then this may be a disadvantage.
The snag is that with most of these schemes the frequency is low and you need large capacitors so in all probability you won't manage to add to much. Give it a try you are probably running well lagging anyway so some compensation may be a step in the right direction. Transformers are not good at low frequency they need to be very large for a low loss, not only will the no load loss be high but I expect the full low load loss will be high as the things need to be monsters to keep I^R losses comparable with normal frequency schemes.
If you are lucky and have chosen an alternator with lots of poles then the frequency may not be so bad.
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