And that the enemy can still cap while their flag is away, that is really bad and contradictory of team gameplay.
It is a bad thing on maps where caps happen fast, but on maps with hard enough capture progress it is fine to me. There can still happen alot in those moments.
Either you cap first and get the critbonus first, meaning you can wipe out half the enemy team.
Or you cap second and get your team thinned out. You still get the capture but you gain less because you were slower. The setback at least isnt as harsh.
And in some cases people just delay their capture until their team was respawned or when they are again heading for the intel so you can deliver a heavy counter punch.
It involves enough tactics for slow capture systems.
Only when captures happen fast that system is good to slow down the captures. Especialy since a 3v2 capture finish in such way is rare in tf2. Many times its 3v1 or 3v0 because 1 team is generaly stronger, and with such systems to prevent capture you are more likely to make it worse (they finaly manage to get the intel out as losing team, but they still cant cap).
With fast captures a 3v2 can happen very fast as both intels could be constantly away. Where in tf2 the scout in such case would dominate it would also be a huge downside since why would a heavy take the intel if it slows your team down? In such case having the flag is a good system to stall an enemy capture. The heavy in this case is also a better protection which in such situations are more important.
Balance has alot of features and you cant just blame it on 1 part. Most ctf maps in tf2 have multiple problems:
Easy to defend, hard to push (only good teams will ever get a chance to win since with 2 noob teams expect the intel covered by 3 sentries)
Capturing once boosts chaining captures making comebacks alot harder (and for weaker teams its devestating)
Maps are often flawed where classes cant realy perform their roles, as everything is just a bottleneck.
Maps dont promote attacking once you are 2v0 behind. It focusses on defense since its far more beneficial as the stalemate eventualy will happen on anything except a 24/7 server. And as defending is alot easier its the way to go.