Installing 16 SEER equipment may not be the right option since it will be 2-stage but 14 or 15 SEER should definitely be considered. All 13 SEER equipment is builders grade and will have minimal warranties few if any safeties. The higher quality 14 or 15 SEER units are without a doubt worth the extra money just for the quality of the product.
As to the Clean Effects or any electronic filter system, they all have benefits over standard media filters. The question is do you need them; most benefit of filtration is for the equipment. It will keep the equipment cleaner which will increase equipment life and efficiency. If your family has serious allergy problems then the more expensive electronic filter could be beneficial but for most people a regular extended media filter is more than sufficient.
I do agree that there is no reason in Houston to spend the money for a 90% furnace over an 80% but it is definitely worth spending extra money on a variable speed furnace.
I am curious what company you have a quote from and have you checked their references. Were they recommended by your builder or are you going the owner builder route.