Three4Flinching: Did they do something to change the games besides the pyramides when they put these two games together? I desided to play the MM4 world befor entering MM5 world, so hoping there won�t be any balancing issues.
I played MM4 first back in the day, and then went out and bought MM5 and worked through that. While the first town was extremely easy, I seem to remember the difficulty catching up to me pretty quickly, so I wouldn't worry about doing Clouds first and then Darkside. But like WizardStan said, you'll get to a MUCH higher level in Darkside so doing that first really will make Clouds too easy.
I'm taking a break after finishing MM1, but after I've played through MM2 and MM3 I'll finally return to Xeen and see what it's like playing the two games together. My guess is that being able to warp to Darkside will help in the early game as it gives you a second easy town and maybe some easy dungeons (my memory is a little fuzzy on that) to do if you're having trouble in Clouds. I doubt I'll do too much of Darkside before deciding to just tackle the rest of Clouds though; I feel like Darkside really ramps the difficulty up so you can take your party to much higher levels. I remember the Darkside manual going over some strategies related to the steeper difficulty curve of that game. You'll likely find most of Clouds to be easier, but by all means switch back and forth and try things out.
Also, the third endgame that has you going between Clouds and Darkside is pretty awesome. You're in for a treat.