So they should change the TDF to an omnium format?

FWIW I've won more than a couple omniums and stage races. And I'm a pretty good TT guy. So my view on this has zip to do with self interest.

Omniums are good for promoters. Otherwise, as pointed out, you end up with field sprints that are a cluster. Or races where the field sits on it's hands, rides 15 MPH, chases everything in the top 10, and let's people ride away and finish 10 minutes in front of the pack. The lamest races I've ever been in have been omniums. The absolute worst was with a guy who was one point behind me and literally rode to a dead stop in the crit rather than come around to take a pull. I Friere'd him at the line which made it even sweeter.

No one who wants to win GC can get away with that in a stage race.

And the only way a pure TT beast wins a stage race is if the field lets them. Pretty easy to rip a "TT only" guy apart. I've taken minutes out of guys in a crit, won on a KOM time bonus, killed in the RR and had 2-3 teams get together to attack me when I've won the TT and gotten knocked down off the top podium step. Just takes a little sack and aggressive riding, and a willingness not to settle for 8th or whatever.

FWIW a lack of TT ability is most often on that individual. TT's take discipline, practice, and hard work. Folks with low FTP's can TT quite well, I know several, and I've seen massive improvements in TT ability when folks actually try to improve their TT ability. And using equipment as an excuse is a poor excuse. I can set up a pretty decent TT bike for <$800. I could take that bike and beat guys on $10,000 TT rigs. I might beat them by 1-2% more on my blingmobile.

Again, TT's take discipline, practice, and hard work. Prior to my injury I would ride my TT bike 2-3 times a week, including doing some 2-3 hour climbing rides (actually heading out on the BMC for a climbing ride today). The benefits to working on your TT are numerous and make you a better racer in other disciplines.