Instead of the Jihad they could have had ComStar stoke more division in the IS via the already fracturing alliances and creating more distrust of the Clans that were trying to re-integrate back into IS society. ComStar faked their mechs up plenty of times, it wouldn't have been much effort for them to acquire some Omnis and paint them as Clan So and So to go hit critical targets and sow discord. Likewise they could have further broadened the divide between the Lyran Alliance and Federated Commonwealth after the Civil War to keep them in a perpetual Marik like state with Kurita occasionally raiding into Fed territory to keep them off balance.
With places like the Isle of Skye, Rasalhague, St. Ives and so on, they could have stoked the flames of independence movements within these nations.
The logic could be something like "We're all part of the 2nd SLDF anyway, so why not allow us our freedom to administer ourselves?" while ComStar does this to diminish influence of the major successor houses. An SLDF with 6 major voting members is harder to control than an SLDF with 12, where half of them are tightly bound to ComStar's support, like Rasalhague.
The question is: How can you design this situation to allow for skirmishes between factions, so the "wargaming" aspect of BT isn't lost, but still make it fit the current political setting under the SLDF umbrella?
Based on the old SLDF's history and how they got dragged into the Periphery uprisings and their focus on protection against the Clans, internal struggles or smaller border conflicts could very well be outside of the SLDF's duties to some degree and they don't have the size and power of force projection to get involved everywhere anyway. And ComStar could also be used as an explanation of this situation, given that they act behind closed doors.
The way I see it, there'd be 3 possible conflict scenarios:
Major state vs major state: SLDF doesn't need to become active, cause the opponents meet on equal footing and might actually not want SLDF to get involved.
Minor state vs minor state: dito.
Major State vs minor state: SLDF might act more like peacekeepers and protect cities, while skirmishes happen elsewhere.
This political situation could take notes from NATO and the smaller conflicts in the middle east. There could also be proxy wars.
And if you want to go all out: Make two powerblocks, maybe one ComStar-backed, one Word-of-Blake-backed, who engage in proxy-wars along several borders.
Regarding the ongoing topic about the Jihad itself:
I agree, another Succession War would have been unappealing. My issue is that the setting of BT sort of strives for this rebirth of the SLDF and when it finally happens, it just ges nowhere fast and WoB starts a major conflict with rather overblown assets that they obtained somehow within a couple years.
It feels like the whole SLDF thing just inflated instantly and everything that happened beforehand becomes meaningless. In a way it feels like the Star Wars sequels. After three movies showing the rebels defeating the empire, we're back to square one come the next movie. Many characters got trampled by the Jihad.
I'm fine with the idea of a Jihad happening, I just think it would have been better to put something before it (like what I describe above), so the 2nd SLDF has some glory time before it gets dissolved - I would actually prefer, if the SLDF is split up rather than outright getting dissolved.