I've handled both and my recollection is that the soldiers are probably close in scale. The boats in Cyclades are close to the same size as the armies, so don't expect CotE boats to have a chance to work in Cyclades(they won't fit on the spaces very well anyways).
Well you should get it because Cyclades is an awesome game. If the minis matchup, more the merrier I suppose. And I do think they are close enough in scale. Though the Conquest soldiers may be a TAD bigger from my memory. But I just haven't had them on the table at the same time.
You should get Cyclades regardless of the miniatures -- it's just that good! The game mechanics are tight, and there are many paths to victory without one being out of balance. Good stuff. Probably my favorite boardgame.