A big part of the decision is mission and location.
The C is great at lower altitudes and shorter flights (less than 500 miles). I live in the inter-mountain west and loved my C but it was a little wimpy getting over a few passes in Colorado and Nevada. An E is nice if you are going to spend a lot of time over 10,000 feet or need to get to over 13 to 15K to clear a pass. The extra speed for longer flights is nice with the E but on shorter flights the total time (getting to the airport, pulling the plane out, etc., etc.) is not very different with the C or E. If you are flying now an then for fun the AP is nice but not necessary. For many hours per years or as an IFR platform you will want one.
Define your mission and how much you want to spend. After the money is paid you will not miss it but you might be wishing for the upgrades if you don't get them.