Yeah, Call to Arms is one of those where the good just so far outweighs the bad. An abosolute classic episode. I missed the episode the first time round and just went straight into season 6, which kinda took the shine off things for me a little. Subsequent rewatches have put everything right though.
The sense of dark forboding is very strong; nothing will be the same. It's just all so much better than the majority of Star Trek cliffhangers.