It is the old comparing apples to oranges story. They are both good, although, so totally different in every way; type of cuisine, mood, style, and almost everything. They are so far apart and yet so good doing their own thing! Just pick the one you are in the mood for on a particular evening and go for it.
I just went to Mako a few weeks ago (we sat at the bar overlooking the open kitchen). Food-wise, we thought it was excellent! Really well prepared, seasoned and just delicious dishes. Note, you pay for it in the end.
I'm also a big fan of Lucques and I don't need to explain why since you've been there before.
I think it comes down to atmosphere and what kind of mood you're in. Mako is a very casual and open restaurant and Lucques is more intimate and romantic.