We remodeled our kitchen about 7 years ago and faced the same problem with the stove/oven/microwave placement. The pictures in the link show what we came up with. The low oven is a bit of a compromise, but like you, we have a small kitchen, so it's full of compromises. We do use the oven, and the height has not been much of an issue. Getting the m/w up off the counter has been great, and the room for a toaster oven below it is a big bonus. There is still room in front of the toaster oven for a landing area for food from the m/w. We are also able to have a real vent hood over the cooktop, which I consider a must. If you're planning on putting the oven under the cooktop you need to check carefully for both clearance issues and mfr's statements on suitability for such an application. There's another discussion here about that. Good luck.

Here is a link that might be useful: Steve & Joette's Kitchen and Bath Pix