DescentBB

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May have had something to do with the new engine. Most likely they wanted weapons that showed off what the new technology could do.
The biggest casualty was probably D2's omega cannon. That could have been super useful against the small fast enemies that were everywhere in D3. Both EMD and its own redesign are far less so.
Helix would be a waste of energy with at least three out of five shots probably missing most targets and phoenix would be far more difficult to control on all the different angled surfaces, circular tubes, and protrusions of D3's map geometry, not to mention trying to aim at something you can't see was already a challenge even with the enemies in D2 that were fairly easy to hit when they were in view.

Vauss at least was a little bit more useful than vulcan or gauss, but ammo for all the non-energy weapons seemed to be pretty scarce in D3.

When it comes to Overload though, they've got equivalents of both Helix and Phoenix in that game which work really well, so they seem to have realized their mistake somewhat. Only took them nineteen years.

You can however experience using the Helix and Phoenix in D3 by installing Pyromania. I think it works with the main campaign. But yeah, you'll probably find they aren't as useful as you imagine in D3 due to the large size of the levels and the geometry.

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Yes, the Magnum and the Black Pyro have pretty effective Microwave.

You could kill yourself with the earthshaker just as easily.
Or with the phoenix.
Or the mega in D1.

Accidental suicide via your own weapons is a long tradition in Descent.