Perhaps the BEST B1G Forum anywhere, here at College Football Fan Site, CFB51!!!

My reasoning:

Lake Forest/Michigan:
According to Wiki, the discussion was initiated by James Henry Smart, President of Purdue and the first meeting was January 11, 1895 with Presidents of the following included:

• Chicago
• Lake Forest
• Northwestern
• Illinois
• Purdue
• Wisconsin
• Minnesota

I've organized these to help explain why I think Lake Forest's replacement by Michigan was so important.  The initial seven (above) are three private schools in the Chicago Metro Area and four Public State Flagship Universities.  Note, however, that Illinois is in the same state as the three Chicago schools while Purdue and Wisconsin are both pretty close to Chicago as well.  Only Minnesota is significantly outside of Chicago.  

I think this change is important because with out it, I think that the Intercollegiate Conference of Faculty Representatives would likely have evolved as basically a glorified "Chicago Metro League".  In the actual timeline, Michigan replaced Lake Forest and the institution was chartered with the seven schools listed above less Lake Forest, plus Michigan.  Then:

• 1899 Iowa and Indiana joined
• 1900 Nebraska petitioned to join but got turned down
• 1907 Michigan was voted out
• 1911 Nebraska turned down again
• 1912 Ohio State joined
• 1916 Michigan rejoined
• 1946 Chicago left
• 1949 Michigan State joined

In an alternate timeline with Lake Forest in and Michigan out, I think that likely additions would have been schools like Loyola-Chicago and other Chicago Metro Area schools and the league would have been successful at first but eventually proven too small for the large public "flagship" schools of Illinois, Purdue/Indiana, Wisconsin, and Minnesota.  

Also, what would Michigan and Ohio State have done if not included in what became the B1G?  Maybe their rivalry looks to the East and adds Penn State much earlier while also attempting to compete with the Ivy League schools which were the major football powers of the day.  

My reasoning, USCe and Arkansas to the SEC:

Frankly, USCe and even Arkansas aren't all that important.  The bigger impact of this change was the beginning of what we have now.  With those schools, the SEC was able to split into divisions and stage a lucrative CG.  IMHO, that was what ultimately led to the moves that got us to where we are now.  

Not to mention that the Western Conference was the precursor to the NCAA as we once knew it.

It is largely irrelevant now when it comes to Football at the P5 level.

True, and I agree that it is largely irrelevant today but it had a lot to do with how we got from 1890's wild west to where we are today.

i'd throw in sec split from socon. socon was a super conference similar to what it feels like we're heading towards today. 23 schools, and most are top half p5 teams. bama, au, lsu, fl, tenn, uga, clemson, ga tech, virginia, va tech, kentucy, vandy, unc, nc state, maryland, ole miss, msu, duke, and usc were all in socon.

that looks like a not unrealistic version of something we could end up with in near future.

sec split off for a couple of different reasons, but travel, admissions, and athletic budgets were all part of the decision.

i could see a reality where that split doesn't happen, and the b1g/pac combine similarly, and we end up with an american/national divisional setup like nfl/mlb. have the rose bowl/sugar bowl for div champs and then a +1 superbowl type game for cfb. at the time, college sports were much bigger than pro, too, outside of mlb, so could see this being the dominant sport.

The SEC had teams that wouldn't play each other even after that.  Georgia Tech would not play a Mississippi school in football, period.  I think Tech has played Ole Miss four times, all in bowls or OOC.

I still can't believe the B1G added Rutgers.  

This is a good addition.  Part of the reason I didn't include it is that, to the best of my knowledge the old SOCON was an oddity that didn't really function anything like what became the B1G and like conferences function now.  IIRC, some schools wouldn't play others or wouldn't visit others and this was all acceptable within that framework which just seems odd. 

that's true. but conferences had uneven schedules all the way into the late 70's if i remember right. maybe 80's. i know bama won an sec title in 70's due to having played 1 more game than rest of conference (also was undefeated and only other team with argument was on probation, so not controversial, but could have been). i'm sure there were come controversial ones.

socon split from even bigger siaa conference, which was a bumbling mess of a conference that couldn't decide if it wanted to exist or not.