I feel differently. I think the Logic compressor is very good, better than a lot of third party plugins I've owned. It's the one plugin I know I'll never replace.
I feel that Logic lacks a flexible saturation plugin, a decent algorithmic reverb, a good sounding chorus plugin.
The Amp Designer plugin is just OK (but the Bass Amp Designer sounds good).
If you need to clean up files you might want to look into Izotope RX or similar as there's not much to help you in Logic (the denoiser is pretty useless).
I think the included synths sound good, but the GUIs are no fun, especially Ultrabeat and ES2. So a good sounding polyphonic synth and a drum box with nice GUIs would be good additions. I also think some of the included "real" instrument samples are dated, so Kontakt would be another thought if you use a lot of sampled instruments.
Mostly the plugins are excellent. Out of 60+ effect plugins, there are about 40 that I'll use happily. As far as instruments, I think the ESE, ESP, ES2, Retro Synth, Sculpture, Vintage B3, Vintage Clav, and Vintage E-Piano all sound great. The ESX24 is also very capable.