Version 1.0.05 addressed concerns about upgrade path knowledge/information among many other things, and Version 1.0.06 focused on more gameplay variety through other means.
Here's the full changelist, then I'll go over the two big additions:
Added Shuffle Enemies option to the Difficulty menu (complete 5 runs or 1 on Elite to unlock)
Updated some unused enemies to function a bit better, and scaled a few on higher worlds
Updated some world 1 enemies to be tougher on world 2+, and some world 2+ enemies to be a little easier on world 1
Updated Swap Meet modifier allow you to change to alternate power upgrades on vehicle configure screen (and fixed some issues that caused)
Renamed Exchange It modifier to Swap Meet (and updated the description)
Make sound for invulnerable not high-pass
The smaller of the two significant changes is allowing players to use Alternate Powers for each of the vehicles (including the Guardian). Each of them has 3 new powers available, if you have the "Swap Meet" modifier activated. This was the easiest and safest way to allow more power choice for each vehicle. The Scorcher having unlimited energy (essentially) meant I had to pick 3 powers that wouldn't break the game for it. Every power is now present on 2-4 new vehicles.
SHUFFLE ENEMIES
The bigger change is the new "SHUFFLE ENEMIES" toggle on the difficulty menu. When this is enabled, the game replaces enemy spawns (for the whole run) with a random one from the same "class", and slightly adjusts the spawning/etc if there's a big power difference between the old/new enemy.
In addition to the existing enemies, a number of unused enemies were added to the shuffle pool (4 total I think), meaning you'll see some new enemies on occasion. I also adjusted some enemies to have slightly different difficulty on world 1 vs. later worlds.
I've played a number of runs (full and partial) and it seems to accomplish the variety goal quite nicely, but I'll continue to try it out. Feedback on particular enemies being too easy/hard on certain worlds is certainly welcome.
LONG-TERM VARIETY
I've been thinking a lot about how to add more variety to the game recently (was the most common complaint aside from wanting the Ultra Library in the pause menu), and these two changes address that in the most effective way I could think of.
I considered many other solutions for new songs/etc, but all of them will require a large amount of time to do. I hope to come back to that task later this year after I've had more time to think about it. For now though, this is about as much variety as I can squeeze out the current game.
Thanks to everyone for all the feedback and suggestions! I think versions 1.0.05 and 1.0.06 really pushed the game to be the best it can be (in a reasonable amount of time).
Luke