Hello! Yes, it is alright to say "having said that" in this case. "Having said that" can act as another way of saying "with that in mind" or "even though". For this certain scenario, another good term to use could be "However": "However, I still think he has many good ideas." You could also put "however" at the end of the sentence if you choose not to put it at the beginning. It would have to be preceded by a comma. Hope this helps. :)

'Having said that' works just fine. This is more of a conversational phrase, so just be aware that it's awkward in writing. Another option (that I use often) is 'That being said'. Of course, it can also be simplified to 'However' and its many synonyms. Hope this helps!

i'd have said simply. i disagree with him on that point, but i still think he has many good ideas.

Having said that is common usage = despite what has just been said = but

I would say the closest thing to "Having said that" is "That said". Having said that == That having been said == That said. (It is nothing but the passive of "Having said that"). I've heard both "Having said that" and "That said" in company meetings numerous times.