Late to the party but I'm going back to the original premise of "what gives the player impetus to split his/her fleet?" Nav Points, as is, provide combat incentives but that's only one path in creating meaningful choice as it pertains to tactical positioning.
Combat bonuses are one category and we've been discussing them at length. The balancing act, as mentioned, is not making them so good that the force that controls them has a unmitigated advantage but not so weak than that you can avoid them altogether with little loss. Direct combat bonuses such as speed or weapon range (current) are some of the god-stats but so would something like "+10% damage" or "+15% Damage to Shields." These are strictly binary positions though and it would be nice to see something a little more graduated.
I liked the idea of "capture and hold" where the initial bonus is small but grows over time, it doesn't give either side much of a change in position until the battle becomes more mature and as the bonus grows, so does the incentive to hold the point or capture it. If, for example, there was a Nav Buoy that was initially +5% Damage but grew to become +35% Damage over the course of 3 minutes (and this was displayed to the player as a bonus or as counter-intelligence re: the enemy), the bonus and the area of space around the Buoy become gradually more valuable. If the AI was taught that "above 15% of X Bonus, prioritize this point" and made a bee-line for your captured point or drew back to defend their own mature point, there would be more dynamic battlefields. Of course, it would be possible to abuse the AI behavior but if there were multiple points and all were semi-equally valuable, it would be more difficult to do so. I could see Skills promoting this kind of behavior, as well, such as accelerated maturing of points or faster capturing.
In a completely different vein, splitting up fleets could be done via non-combat incentives. Fighting over derelicts, civilian ships, cargo pods, etc. would have more campaign-oriented outcomes worth splitting your fleet over. Imagine three abandoned Phaeton fuel tankers spread out over the map and if you can take and hold that area of space for a set amount of time (or while also defeating the enemy), you get to keep their cargo or even the ship itself (without D mods!). The caveat is that purely defeating the enemy doesn't net you all three: you have to constantly hold the point with a ship. Or something like that.
Or, in yet another avenue, create more battlefield terrain. Nebula are a start but they don't offer a significant advantage or disadvantage for full fleet actions. If you're fighting in Asteroid belt, maybe there are multiple large/stationary asteroids that can't otherwise be broken up, thus it shrinks the battlefield and forces the player and the AI to adjust tactics. Or, as previously mentioned, have a station in the middle that is "impassable terrain" that can also be captured to provide, say, anti-Fighter PD. The issue with terrain is that much of space is well, empty space, and arbitrarily adding terrain feels a bit disingenuous. I guess the way around this is to provide "points of interest" that the player and enemy fleets will converge on so that fights are in areas of space with debris, asteroids, coronas, etc. If nothing else, it will make some fights near planets and stations a bit more varied.