To me, if the Jags went to LA, I think the most likely scenario is that they'd stay in the AFC South for a while, kind of like the Cardinals in the NFC East all those years. The division alignment as it currently stands is really good, both from a geographical and rivalry standpoint. I also think the Rams are too entrenched historically as an NFC franchise to shift to the AFC.
If they did move the Jags to the NFC West (I agree that the former AFL bloc in the AFC West won't get broken up under any circumstances), I think they would shift either the Panthers or Bucs to the AFC South (Panthers because they came in the league with the Jags so that conference offset makes sense, Bucs because their first season was in the AFC), and the Rams (by default) get shifted to the NFC South.
I don't like those moves though, so I'd "penalize" the Jags for moving to LA by keeping them in the AFC South and making them make 3 cross-country trips for division games.
While I could possibly see San Diego move out, Denver/KC/Oakland will never change. I'd change the Jaguars to the Los Angeles Cougars.
I pretty much agree with what you're saying, but the geographic/logical step IMO is for the Rams to move to the AFC South. Nothing else makes sense to me. You aren't taking Seattle/SF/Arizona out of the West, but that's where the LA Cougars would belong. You're not taking the Chiefs out of the AFC West.
By default, the Rams come out of the West, where do they go? Certainly not the NFC North or East. South makes some sense, but geographically St. Louis is too far. The AFC South would be Tennessee, Indianapolis, Houston and St. Louis, pretty much the middle of the country. I might see moving Indianapolis out of the South (geographically, it shouldn't be there anyway), but there's no better place for it.
OTOH, you could switch to 4 divisions of 8 teams each. East/West Conferences, North/South divisions.
NORTH EAST
Baltimore Ravens
Buffalo Bills
Cleveland Browns
New England Patriots
New York Jets
New York Giants
Pittsburgh Steelers
Philadelphia Eagles
SOUTH EAST
Atlanta Falcons
Carolina Panthers
Cincinnati Bengals
Indianapolis Colts
Miami Dolphins
Tampa Bay Buccaneers
Tennessee Titans
Washington Redskins
NORTH WEST (This division rocks for historical rivals - and horrible owners)
Chicago Bears
Denver Broncos
Detroit Lions
Green Bay Packers
Kansas City Chiefs
Minnesota Vikings
Oakland Raiders
Seattle Seahawks .
SOUTH WEST
Arizona Cardinals
Dallas Cowboys
Houston Texans
LA Cougars
New Orleans Saints
San Francisco 49ers
St. Louis Rams
San Diego Chargers
The Playoffs go to the 2 division winners getting byes, next 4 get in.