I have been asked several times by people considering a rotary installation, which engine would I choose if I were to start all over right now. The short answer is a normally aspirated 20B for my purposes, but to make an educated choice for yourself here is a discussion of the possible engines. There are really 3 basic possibilities- the 13B, the Renisis, and the 20B. Any can be turbocharged. Turbocharging is a separate issue, but also plays into which engine you might select.
But first, a few words about horsepower. After all, that is everyone's first question- how much horsepower does your engine make? The answer, truthfully and unfortunately, is "that depends." The Mazda 13B will make a wide variety of h.p. depending on the installation. On one exteme there is the example of the drag racers getting close to 600 h.p. out of a 13B, while on the oppisite end a poor instalation might achieve as little as 150h.p. from the exact same engine. The devil is truly in the details, but it is a reasonable statement to say that the average guy should be able to get about 180h.p. from a normally aspirated 13B in aircraft use. Meaning that if you are a typical guy like me, and make a solid effort to make a nice clean installation you can expect in the neighborhood of 180 h.p. (as measured by performance compared to lycoming powered aircraft). In general, there are 2 ways I can speak about available horse power, what I have read and what I have found in my plane.
Other people's experience includes Tracy Crook who pretty easily beats all 180h.p. RV's at Sun-n-Fun. Tracy feels he is comming up on 200 h.p. from his normally aspirated RENISIS. Powersport claims 215h.p. from their periforal ported 13B - a very reasonable (if not conservative) claim given the experience of periforal porting in the racing community. Perry Mick estimated somewhere around 150 h.p. with his direct drive ducted fan. Chuck Dunlap and Bill Eslick both have normally aspirated rotary engines in their RV-6s that perform something like the 160 h.p. Lyc RV-6's. John Slade seems to be getting around 250 h.p. out of his turbo 13B Cozy with no cooling problems, just turbo longevity problems. Ed Anderson is probably the best example of the variable h.p. that is available. He has an RV-6 with a n/a 13B engine that now makes about 180 h.p. Howeverseems to somewhat best 180h.p. versions.
My airplane is turbocharged which opens up a whole can of worms. The turbo RX-7 that donated my engine was rated at 200h.p. and that is about right for peak h.p. when I was using the stock turbo. Unfortunately, so far I cannot cool that much h.p. continuously. I am limited to about 180 continuous (less than that when it is hot outside - but am currently working out cooling system changes to allow over 200 h.p. continuous).
1) 13B - this is the engine I have. They are very readily available, inexpensive, and parts are cheap. There is also a huge supply of aftermarket parts and accessorys. Most notably, the turbo manifolds are numerous and inexpensive. Other available add-ons include flanges, intakes, superchargers, pullys, and the like. This is the easiest engine to turbo charge and the cheapest to build. However, some of the stock engine parts are starting to get hard to find, as this engine is no longer in production. Rear end housing are one example. It is still easy to get new rotors and rotor housing, quality e-shafts, and most other internal parts. However, it is only a matter of time until those things start to get harder to fined. I would guess that by 2020 many of the parts will be nearly impossible to find. If you want to turbocharge a 2-rotor, this is still probably the best engine if you do not have easy access to a full machine shop. This is still also the best choice to keep the costs as low as possible. It won't be too dificult to change to a renisis in 15 years if parts become in short supply. By then, the Renisis will have plenty of aftermarket parts available.
2) The RENISIS engine out of the RX-8. This engine is so new that you will still probably pay a premium for a good used core. There are also very few after market add-ons like turbo manifolds and intake flanges etc. None the less, the minor improvements and projected availability would make this the best choice for the typical builder who wants a normally aspirated 2-rotor.
3) The 3-rotor 20B. This engine will make 50% more horsepower than the 2-rotor versions but the weight gain is far less than 50% more. These engines are more difficult to build, and re-build. However, they make a very nice alternative to a turbo 2-rotor.