I don't see that much difference. I finished 7th in my first season then signed 12 players and moved out 15 players and went on to finish 2nd. I think the quality of players you sign can overcome the team chemistry dropping.
One weird thing I've noticed is that although team chemistry may reflect the new players, match preparation does not seem to, so signing (almost) all new players is actually easier than when you start a new game, which though not easy, isn't too bad either.
That said, I've often found a slump awaiting after I bring in 5 or 6 new faces even though morale seems high. I think the new players do take some time to adapt and if in key roles (playmaker for example) it can be 4-8 games before you start getting the best out of the new team.
I signed a guy in my game who was pretty decent but potentially excellent. For the first few games the assman said he was struggling to blend in, and his performances were around the 6.5 mark. Dropped him down to the bench for a few games, then when he came on as a sub once he lit the game up. Started him the game after and he's been on fire ever since. I noticed just after he went on fire that he was no longer listed as 'struggling to blend in.' I can only assume that once he blended in, his performances improved to reflect this.
Of course, how long it takes them to blend in depends on many factors like adaptability.
It seems to vary. In my FC United save, I replaced pretty much the whole team before any matches in the first season, and the team I bought still played brilliantly and won the BSN with ease. In my Cambridge United save, I replaced seven players, and my team performed badly for a few games (maybe due to problems blending, or maybe not). After those games, individual performances started getting better and we were soon in winning form.
The drop from team chemistry when I sign lots of player normally impacts my team for about the first 8-10 gamres of the season - so in the long run it is worth it, but it does cause short term problems
I usually sign a huge number of players when I join a club, then stick with them for the near future. It makes the first season a bit of a write off but after two or three seasons I really reap the rewards.
You just need to make sure you make it though the first season without getting sacked
Not always, I've has a few good runs after a lot of changes, usually after arriving at a club and promotion, however if you do assemble a load of good players, you sometimes see an incredible performance boost in the second season, so I don't shy away at bringing in loads of really good players if they're out there if it means a clear improvement in squad quality, knowing that if I don't reap the benefits immeditately, chances are it won't be long.