If there were one thing to change . . . it's tough, but I think anyone could get behind this one.
Go back in time and highly suggest not using those certain 'Mech designs.
To be fair to history though, at the time they did use them it was perfectly above-board and legal. Not until a certain company decided
their license trumped everyone elses license was there any problems.
But yeah, still probably a safe one to do, as far as meddling with time lines go.
Now for my personal one, which is of a much more controversial nature and, again, just my personal opinion: Everything after the 4th Succession War has to go, and we'll start over from there. No Clans, no Civil War, no WOBblies, no Jihad, no Dark Ages. Just the warring states of the Inner Sphere going at it with ever-so-slowly increasing capabilities.
3025 BattleTech is my personally preferred era; I never even liked the Clans when they were first introduced with their power-not-so-much-a-creep-as-a-rushing-torrent, their weird we've-been-gone-300-years-so-of-course-our-society-is-completely-changed, and their übermensch tendencies. Post-clan gets even weirder for me, it just makes me want to get back to the original setting, with the neo-feudal warlords battling it out in centuries-old, poorly understood and poorly maintained war machines. That's where the magic of the setting lies for me, not in assembly-lines worth of new designs pouring in (and out!) over the Inner Sphere border.
All that being said, I take heart that Jordan is on record saying he'd like the chance to fix the power-creep of the later eras, and who knows? HBS might be the place and BATTLETECH the game that makes it happen - if that happens it might even make an old 3025-diehard like me like the Clans.
Edit: Oh, and just for clarification: I fully appreciate that there are fans of later eras out there that love "their" era just as much as I love "mine"; that's a given, and no disrespect towards them intended. The greatest thing about BattleTech's disparate eras is that there's always someone that utterly and truly loves them, even the less popular ones. That's a testament to Jordan and all the other authors' worldbuilding and storytelling skills if anything is.