The first bike I ever owned was a 2007 M109R in blue with the white stripe. I had rode ****** rockets prior, so the looks attracted me. The second bike I owned was the 2011 Rocket 3 roadster. I know a little bit about the two bikes, so here is my honest breakdown:
M109R:
The Good
Sleek modern looks
Vtwin sound
Cool tach
Women seemed to pay more attention to it (likely because it was blue)
better tire choices
Tons of aftermart trinkets to customize it
The bad
The engine is virtually maxed out on power at the stock level. Exhaust and air filters is it. There were a couple tuning companies that did some engine work, but they went under. Reliability became very questionable above 145hp.
The transmissions were for all pratical points garbage. I rode 5 m109rs and none of them shifted decent, and it had a significant known failure rate.
A lot of the bits of metal on the bike felt cheap, and looked it. Considering the price they get for m109rs new I was kind of suprized by that.
The handling was a bore. The m109 riders came up with a new motorcycle sport. Its called high speed peg grinding. They would put hockey puck sized titanium feelers on the pegs and go around turns making sparks. It seemed cool until I realized my bikes stock pegs would grind before I even leaned the bike over enough to make easy turns. I felt like the bike had training wheels that prevented me from pushing it.
The R3 roadster:
The good:
classic looks work well
The engine is a work of art and has a unlimited potential to produce power.
The transmissions and planetary gear system is stout. Shifts very good compared to most crusiers
riding 2 up is comfortable
Not everyone has one, they are rare here in milwaukee
Great handling. I could easily push 20mph more into corners and not rip the exhaust off. Then I found out I had the shock preload adjusted too low for my weight (270) and once I upped it I never ground pegs again. My balls limit my lean angle. At this point it honestly scares me to think of trying to grind the pegs the whole way through a turn, I don't even have any chicken strips on my rear tire as it is.
The bad:
Minimal aftermarket parts
Limited tire choices
"Is that a harley?" I get that a lot
Doesnt get as many looks as my 109r did, but black and chrome vs bright blue is a no contest for attention grabbing.
The sound of it isn't bad, but I miss the shake and rumble of the 109r
When you look at the big picture, the m109r's mechanicals are far inferior to the rocket 3. It has a weak transmission, weak engine (as most v-twins are), and has very limited power potential. The handling is so limited by the low peg clearance on the m109r that it flat out would get blown away by the r3 in corners. All things said the r3 has the 109r beat without discussion from a mechanical end. The r3 has numerous 240 hp bikes, and 300+ hp bikes that have lasted. I haven't heard of people blowing up the transmissions in the R3 (clutch baskets sure), compared to stock m109r that have transmission failures and good luck with a modified bike. Its really not up for discussion which bike is mechanically and handling superior out of the box and which one has more potential.
However if all that mattered is raw data then nobody would own a harley compared to the better performing bikes out there. The reality is a bike can speak to you and it doesn't ***ing matter what someone else thinks of your bike. The styling on the 109r is bad ass and completely different then the R3. If the 109r had a stronger engine and trans, I would have kept it and put up with the lack of lean angle. However it doesn't and thats why I ride the r3. As a total package the r3 roadster does everything I want. I can ride 2 up at 100mph with my girl, and she is comfortable for long distances. I can tackle canyons and mountain roads without fear of running out of lean angle. I don't have to shift gears to always be in the power band. I am not worried about the reliability of the R3s mechanicals. From a cruiser standpoint I haven't found another bike that has the potential the r3 has.