General Sci-FI
• Human expansion should never stop once it has started. The Periphery should still be growing in leaps and bounds. Lower tech, but growing outwards. Even if we control jumpships people would use slower generation ships to expand the frontier.
• Comstar. As designed Comstar didn't work. Against individual planets they have a lot of power, cutting off a single system means no trade. However against a 200 planet empire the rulers have the resources to find a way around this. Either seizing the HPGs or designing thier own, over 500 years and thousands of planets there is no way Comstar can stop the reinvention of a known technology. Too much incentive for the Successor States to get around them, too many people and places to control and monitor for Comstar.
• The Clans Culture changed to much, to quickly, and to radically for what should be conservative folk. Let the clans invade, set their exodus back several hundred years and from some strange religious movement to begin with. Not "The Military" and only 2-3 generations removed.

Warfare
• Loss of Technology. No one fights a war against a technologically equivalent foe where both sides lose technology. Either one side wins and progresses or both sides stop long before that point.
• The High ground. Having space travel means whomever controls the high ground wins the planet. More needs to be done to limit warfare to planetary surfaces. Maybe a Dune like Guild (ComStar?) controlling all the Jumpships and disallowing space combat but they will transport you anywhere for a fee.
• Missiles. Dear God how badly battletech missiles suck. I'm gonna get you with my Catapult that fires Katusha rockets surplused from Russian WWII stocks. Mechs needs to have built in stealth/ECM.
• Aerospace Fighters. So I can overlook mechs as being better technology than vehicles, but we can we build an aerospace fighter but not a tank with equivalent armor/IS/safety for the crew? Want the mechs to be the kings of the battlefield then dont make aerospace fighters flying mechs.
• The Clans Warfare. Even if they are better than the IS forces. They way they fight vs the way the IS has been fighting means the clans take 1 or two planets before they are stopped cold unless they drastically change thier tactics. See the Powell Doctrine. No one fights like they do and wins.