WDADU > SC & BCSL
Why? Because there is nothing on WDADU that makes me roll my eyes or cringe.

It doesn't matter to me, whether the transitions on WDADU are less smoother than on later albums. It is an album from a band, which is full of enthusiasm and talent, but not really experience. What do you expect? It couldn't be Images and Words yet, but it is When Dream and Day Unite and it is a fun album to listen every then and now.
That being said, I like SC very much. Probably my 6th favourite studio album.
Repentance is by far the best song on Systematic Chaos.
After ITPOE (I consider it as a one song) and Prophets of War.
Talk about controversial? Ha!
I know some songs are better with JLB from a technical standpoint, but i think (with the exception of the Killing Hand which is better by James 92-93 era) but i think that Charlie is good on other songs. Especially Status Seeker, this might be his best DT performance imo.
YOU ARE... correct. I should look for live versions of WDADU songs from 90s. The Killing Hand from LATM would be a top 3 song, and I love James's vocals in AFIL, from the same album.
But when it comes to WDARU, I prefer Charlie (expect those two). James's voice just doesn't suit Light Fuse and Get Away as well as Charlie's.
And yes, I love the vocals in Status Seeker.