I would be interested to know two things.
What is the best Amiga specific FPS, is it actually AB 3D v1?
Personally, I'd say it was one of the most ground breaking of the "first generation" of amiga "chunky copperscreen" doom clones (said games all used various copper tricks to fake a chunky pixel display, later games just used chunky to planar conversion which by the time you get to 68040 takes no more time than plain writing data to chip RAM). Pitted against the likes of gloom and fears, it stands right out, both technically and in terms of atmopshere.
Technical highlights of AB3D1 included (but are not limited to):
Arbitrarily angled zones
Contrast with Fears, which was largely "rectangular" (even later titles like Breathless and Genetic Species followed the simpler wolfenstein-esque "by blocks" method of laying out maps).
Variable height zones, with lifts, stairs etc.
Contrast with Gloom (and later, Genetic Species) in which each level was completely flat.
Vertically split zones
Allowed for two levels in the same zone. Doom itself didn't have this. I think only Duke Nukem 3D had a similar feature.
Shaded texture mapping
Of all contemporary amiga doom clones, this was pretty much unique to AB3D1 and improved in AB3D2. As well as being textured, walls and floors were Gouraud shaded from vertex to vertex to produce smoother lighting effects. Doom-style sharp changes in lighting between zones were still possible.
Transparent water / refraction
As above, no other amiga doom clone had water effects to match. It was a shame that the water ripple texture animated per frame, which made it look a bit too fast on quicker machines, but overall the effect was very nice indeed. To be honest, it's only since the advent of "refraction shaders" in modern 3D that I've seen it done significantly better. A nice touch was that once you went under the water, the palette was subtly modified and the audio filter enabled. The liquid effects in Doom were frankly rubbish in comparison, nothing more than animated floor textures that you didn't even sink into to any depth. Quake's were better, but still lacked any transparency (pre OpenGL at least) and while the screen-space refraction effects under water were cool, they were totally unrealistic. Refraction only happens at the interface between materials like air and water.
Polygon models
Like Doom and the various amiga doom clones, the game mostly 2D used sprites for enemies, collectables etc. However, it was capable of using models too, though the only examples to be seen are the various wall lights and the mid-game boss, a grenade lobbing robot walker.
Pseudo RGB rendering
Probably not unique to AB3D1 as a "chunky copperscreen" engine, the hardware banging display code allowed it to basically render all the visuals using 4096 colours, essentially giving you a pseudo RGB 12-bit mode. The benefits of this are a bit subjective as the colour resolution is only 12 bits but no doubt it helped with the shading effects.
Beyond all these, it just had the right atmosphere. Tense and uneasy with the prospect of a sudden and violent death round the next bend...
I should point out that you can't criticise Gloom for it's gameplay however, it was enormous fun, especially in two player mode.
AB3D2 was likewise technically very impressive. As a 1x1 pixelmode capable C2P based renderer, it went back to 256 colours only but thanks to a careful palette selection (and the fact the palette entries are 24-bit) and the use of dithering (which I never noticed until getting a proper monitor), it looked very nice. The shading had been improved allowing for realtime lighting effects from weapon shots, explosions etc. Polygon models featured a lot more, including all weapons and several enemies. Even the 2D sprites were given light maps to make them fit better. There was also a greater freedom of view using the same sort of look up/down technique that was used by Duke Nukem 3D.
Unfortunately, the game seemed somewhat rushed. It probably didn't help that not enough people were working on it. Frankly you need a 68060 (or emulator) to play it to it's full potential, on my 040 it had moments where it was very slow. A lot of the sprites seemed hurried and didn't really have enough animation or directional views. Unlike sprites in Doom, which typically had up to 8 unique views for each animation frame (for viewing at different rotational angles), there were only 4 views. The level design just wasn't as interesting as the first, either.
For all the technical feats, there was a definite sense of let down. I still enjoyed it but felt a bit sad that it could have been that much better as a game too.
What is the best Doom engine to run Doom WAD files on Amiga A1200?
I haven't played in a long time but on my old 68040, DoomAttack was easily one of the most fully featured, including a lot of features not present in the original version of Doom, such as being able to look up and down with manual aim (as opposed to simply facing the general direction of the enemy and firing), jump etc.