The stock Bonneville isn't bad as it comes.... But! it can be so much better....
As far as the suspension goes...I know alot of people like the Ikons...I went a different direction..I put Progressive Suspensions dual rate fork springs and their 440 series shocks on my Bonnie and it absolutely TRANSFORMED the handling, stability and comfort of it...The Ikons don't come close...
Brakes...install Spiegler braided ss line and EBC HH pads... A good improvement on the stock set up...
Another comfort upgrade you can do that is not very expensive, if you like the stock seat, is to have to have it refoamed with a quality foam. I had mine done by Sargent Cycle Products in Jacksonville Fla. with their "super cell" foam and it is worlds better than the stock stuff...
The neat thing about doing mods is that they can be done in steps... But after pipes and rejetting, you'll get the best bang for the buck on the suspension...Have fun and enjoy