The Excel is basically the III/VI/VII fuselage combined with the V (5) - tail and wing (well that a bit exaggerated...)
The III was the first "big" fuselage Cessna built. The Excel/XLS and Sovereign do share it. (Sovereigns longer, but still same diameter 1,73cm)
The big difference INSIDE the Excel and the 650 is that the Wingspar is not intruding the cabin in the Excel (560XL or 560XLS btw.)
Outside it is the as said before the more or less straight wing compared to the sweptback wing of the 650 and the T-tail. The 650 has 2 wheels on each main anding gear, the 560XL/XLS has only one. both have trailing gear.
The XL/XLS is a relatively good performer but roughly 30 to 50 knots slower than the 650. But it climbs way better and can cruise in 430 or 450 directly. You won´t do that in a III or VI and even the more powerful VII strugles to go up when fully loaded.
Systemwise the 560XL/XLS shares a lot with the "small" fuselage citations (500,550,560 and 525´s) whilst the 650 is considerably more "complex".
The APU was an option in the beginning, so there might be a few 560XL on the market without APU. but most were with APU.
Speaking of the APU: the 650 has a lot of different APU´s installed, some for Ground use only, some with a hydraulic pump some without. Check with a EXPERIENCED maintenance shop which to avoid, there are some that are more troubled than others.
The Excel is for sure the cheaper aircraft to operate. And it can do most trips the 650 does - but the 650 looks way better no doubt.
The Encore is the V or Ultra with different avionics, engine and gear (trailing)
And has no APU.