Honestly, it depends. As you know from your research:

The Encore has a light jet cabin (small), while the Excel has a midsize cabin (almost stand-up). The Excel also has an externally-serviceable lav.

The Excel has an APU (well, most do anyway...) while the right engine or a power cart is the Encore's GPU.

The Excel is slightly faster than the Encore, despite having largely the same wing. The Excel also books having slightly more range than the Encore.

Both are great runway performers, though the Encore outclimbs pretty much anything Cessna makes with the possible exception of the Sovereign.

Encore burns less fuel and has lower overall DOCs than the Excel. Its ramp fees and minimum fuel purchase at FBOs will probably be lower, too.

Excel will have a little more baggage space than the Encore.

You can fly an Encore single-pilot with a SP Waiver to your CE500 type rating.

As a pilot, I'd love having an APU and passengers normally like a bigger cabin, so in that case its advantage Excel...but if operating costs are a concern then the Encore provides nearly equal performance for less money.

Perhaps some NJA pilots could share their opinions on both airplanes?