My 2004 R1 was one that I did NOT regret selling.
I bought it new, to use as my Open Supersport and Open Superbike race bike, as well as to instruct at track days and in our racing school, the first year this generation of R1 came out.
I chose the R1 because Yamaha's contingency payment program offered $2,000 per win in each of those two classes, and the exhaust was tucked up under the tail, so I figured it would crash better than it's competitors. I never did crash it.
It handled well for the time and for what it was, but my new MV Agusta F3 800 handles WAY better.
It was my last fully analog bike, with no electronic rider aids.
The stock shock was utter crap. I scored an Ohlins built for the Graves factory Yamaha race bikes, and it transformed the bike.
One of the strangest things about these, were that they were big-bore, short-stroke engines with 5 valves per cylinder, PLUS they had Yamaha's "EXUP" valve in the exhaust system. Between those two things, they felt like a 600 with a really big turbo. They didn't make much power down low, the EXUP valve made a MASSIVE hole in the powerband at about 7,500 rpm, and then they ran strong from about 8,000 rpm to the rev limiter at 14,100 rpm. You wouldn't notice the lack of low-rpm power on the race track, but on the street, it was agonizing, especially since first gear was geared for 104 mph. I installed a 4 into 2 into 1 into 2 full titanium Graves/Toobee exhaust system that eliminated the EXUP valve, and a Power Commander to map around it, which gave it another 5-6 peak horsepower, but filled in the hole at 7,500 rpm to the tune of about 20 horsepower, allowing me to ride a gear higher in many places, and shift about half as much.
Once it got old enough that Yamaha quit paying contingency money on it, I retired it to use as a street bike. Eventually I sold it to a guy, and was really bummed to find out that he died shortly after buying it. FORTUNATELY, I then found out that he didn't die on the bike- it was in the shop at the time for maintenance. I was already looking forward to a Ducati Panigale or an MV Agusta, so I made no effort to follow it from there.