So my '16 had Boom1 in it. Is upgrading to Boom2 worth it ? Does anything need reflashed ?
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Yes it would need flashed if you change to Boom II. Boom II's have external digitally controlled amps for each pair of speakers in your system and Boom I uses the heads internal amp.
For the record, I have had two bikes with Boom II systems and they have performed
flawlessly. I am an audiophile and I play my music
loud all the time. Boom II offers crisp highs and powerful lows. I have
never blown a speaker (knock on wood!) I don't know if this has anything to do with the longevity but my bikes are always parked in the garage when I am not riding and I live in Ohio so from Nov to March they see little activity?? I also wipe my bikes down with detailer spray every ride or two so they rarely get water soaked.

I have seen some "High End" Aftermarket Systems that sound good with Subs and Amps but for most of the AM systems I hear and see, my Boom II's blow them away, especially in the clean bass department.
Another consideration is the type of riding you do. If mostly at high speeds and interstates then Bass tends to get washed out and the mids and highs are what really count towards what you hear. If that's how you ride then maybe AM systems are right for you? If you tend to ride more at lower speeds then it's nice to have the power and bass of the Boom II for a rich sound.
I personally recommend the Boom II systems if you are considering. As for the cost, buy the parts from a discount dealer and do the work yourself and then just have the dealer flash it.