They've been pretty much nonexistant in PvE and PvP since Y1. I'd love to see them come back. Not sure what the best way to do this would be, but it'd be nice to use something other than Handcannons all the time.
Edit: Wow, thanks for the response Cozmo! Now I'm no game designer, but here's my opinion on what I think should be done.
Aggresive and adaptive frame Pulses are dominating the mid to long ranges where Scout rifles SHOULD thrive. I think both could use a range nerf, but especially aggresive frames. Scouts could also use a straight up damage buff so they can compete with other popular pve weapons.
Auto rifles just need a straight up damage buff to compete in the mid range where HCs thrive. Maybe knock Handcannon range back SLIGHTLY.
The guys below me have way better suggestions, this was just my take. I was JUST talking to someone about how the Valakydyn was my favorite y1 weapon. Glad to see they're being talked about!
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You're right, auto rifles deserve a 0.04% buff. [spoiler]And by that I mean nerf fusion rifles[/spoiler]