Depends what you mean by "fleet abilities".
If they field a ship, then that ship will have all the special rules that apply to that ship (for example an allied Ipsha globe will still have its saving throw and superb manouvrability).
You won't get any bonuses that apply to the fleet as a whole (for example the Drazi's initiative bonus when attacking doesn't apply because it's an ISA fleet commanded by minbari and rangers with bad hairdos, the drazi are just there to support). Equally, campaign-specific rules like the pak'ma'ra's won't apply, even if you take the pak as allies. For campaign and fleet initiative purposes, you always use the ISA's rules, no matter who your allies may be. The only exception to this is that allied ships will get refits from their own race, not ISA ones.