Could this poor flush be caused by the short drop due to it being in the lower level?
As long as the pipe slopes at least 1/8" per foot, that's all it needs.
Fear not, you most likely should easily be able to get everything you want from your Aquia. My suggestion: Call a good, real plumber that has good recommendations and is known there in Milford (not one of these Rooter places that's going to suggest all sorts of digging and piping and stuff). Ask him to snake the main drain line, which may or may not involve pulling the toilet and putting it back in. Chances are that once it is clear, you will have what you want.
I got a recommendation from our member MacPlumb a while back, who is a master plumber in the drain cleaning business who knows good operators around the country. I can ask him if he recommends someone there in Milford. The guy he put me in touch with on Long Island was a one-man operation, totally rocked, did an incredible job at a very modest price for what he accomplished and what he brought to the job, and earned multiple recommendations from me to others, who were in turn quite satisfied. But if you have a good trusted plumber there, use him. It may not be the cheapest route in the short term, but there's a value to getting it done right the first time.
Actually, doing a little research on my own, this guy Terrence has exclusively great reviews on HomeAdvisor, and enough of them (31) to be believeable, one positive review and no negative ones at the BBB, and seems to try to run a customer-focused one-man shop. It's always good when half of the reviewers comment on how professional he is and many call him a gentleman and say that he is who they would call next time. It means that he has made a good enough impression that people are writing reviews to try to help his business. He says if you call him, your call will be answered by a real person (most likely him, I'll bet). He's a guy I would call, and he has a no-charge-if-he-can't-fix-it policy, which is as good as it gets. (and I would just call him, and save him whatever commission HomeAdvisor collects for appointments made on their site; I just put up the link to the site so you can see his reviews and make your own decision).
http://www.homeadvisor.com/rated.KlearKlogsLLC.41614145.html#ratingsReviews
If you try him, let me know what you think.
You indicate that the toilet is located on the first floor, not the basement. Do you have a basement such that you readily can see the piping from the toilet to the main line and the main line out to where it goes off to the septic tank? If so, it couldn't hurt to shoot us a couple of photos of that setup just so we can see that the piping itself is correct. If what you have instead is a crawlspace or something, don't worry about it.
