Cristiano - alot of it comes down to personal preference. There are plenty of opinions you can search here about 22 vs 24 frets, but in general the neck pickup on a 22-fret guitar will give you a little more full, rounded sound for leads, whereas the neck pickup on a 24 fret guitar will emphasize mids a but more.
The 408 is a thicker body than the CU22/24. Both guitars are generally made from mahogany, and have maple caps and mahogany necks with rosewood fingerboards.
Both the Customs and 408s give you multiple single coil and humbucking options. The newer customs will give you 5 sounds (older up to 6) and the 408s up to 8. Some would characterize the single-coil tones on the 408 to be more authentic/telecaster like. Often times the Customs will blend a single coil with a humbucker in the position. Neither are "stratty."
Aside from that, there are a myriad of neck profiles, wood and pickup choices that will affect tone. So it truly is hard to compare.
Personally, I think the 408 switching system is one of the simplest and most versatile out there. Whether you prefer a blade or a toggle, you can still look down and see immediately where you are. The 408 pickups are some of the best I and many others have ever heard. I have heard folks who ALWAYS replace their pickups say that 408s are the first set of pickups they have ever heard that they would not change out.
The CU22/24 are offered with some amazing pickups - the 57/08s (which have the same wire as the 408s), 59/09s and HFS/Vintage Bass. Apples-to-apples as much as possible, if you get a chance to play both, I would say a CU24 with the 57/08s or 59/09s would be the most fair comparison to the 408.
If I could only keep one guitar, it would be my 408-equipped Signature Limited. Followed closely by my 1991 CU24,