Ok, a few more ideas:
Allow a clan to spend some money to fortify a planet so that it takes more defeats to push them off (as a battle for a capital does now). The cost and time needed would have to be looked at to keep it from happening everywhere, and whether or not the two sides would need more players, or just have 2 guys playing a best-of-whatever series.
An example of one way it could work is this:
GoT owns Antarcticus, and they spend $20 to add 1 level of fortification to it. FoR then decides to attack that Antarcticus, and assigns Pitor to attack it. GoT assigns Tiger to defend it, and he plays a best-of-three series for it. Elsewhere, NWO has added 1 level of fortification to Noble Rust. RN assigns mwigor to attack it, and because there is 1 level of fortification, they can also assign 1 extra attacker at a discount, choosing NikTheKid to do so. NWO assigns Maelstrom to defend Rust. They play only 1 game per attacker, NikTheKid wins, mwigor loses. mwigor being the primary attacker, he then plays Maelstrom in a tiebreaker, with the winner controlling Rust.
I know it would exclude non-MAN players, but perhaps there's some way it could be added, such as not counting towards a player's game count or something? Even if it doesn't do much, it'd add Crateus to the war.
If a clan is defeated, instead of simply erasing them, let them keep what planets they have, but not gain any income. Then, other clans could pay them to attack planets for them (example: RN doesn't have enough money to buy any more attacks because they have so many battles going, so they pay the Wanzers, who have lost their homeworld, to "borrow" Three Seven for an attack. If Three Seven wins, RN get the planet). This would let a defeated clan keep playing, and possibly even get enough money to fight their way back to their capital. I suppose this could also be used for non-defeated clans as well, but I originally thought it up for the conquered.
How about each sector having a transport "hub", and the only way into and out of a sector would be that planet. So then, if FoR attacked NWO in a sector with Emerald, Brimstone, and a hub in Wasserland, they'd have to attack Wasserland and take it before attacking Emerald and Brimstone. Later on, after Wasserland and Brimstone have fallen, NWO couldn't liberate Brimstone until they liberate Wasserland, even though they own Emerald. Other options could be 1) having that hub be the only requirement for attacking onwards, so that when FoR took Wasserland, they could attack the next hub in line while bypassing Emerald and Brimstone and 2) having a planet only give revenue if that sector's hub is controlled by the same clan.
Assuming the hubs were all bigger planets (Wasserland, Rust, New Paradise, Anubis, maybe Crateus), this would remove a lot of the strategic significance of the little planets, so we wouldn't have to take them out of the war. Come to think of it, it would also allow the inclusion of Bizarria...sure, it'd be simple luck as to who won it, but it's not like it would open the way towards a clan's core. Plus, it'd make Redfox happy
I hope all this at least pretended to make sense.