A year and a half back when the input jack problem first started popping up, my line-in went, so I switched over to using the mic input for about 6 mo. until I finally sent it back to Roland. I just reduced the gain on my preamp a bit.
In doing so I found a better combination of preamp & R-09 gain settings so when I got the unit back and switched back to using the line-in on the R-09 (after epoxying the jacks down on the replacement board), I kept running my external preamp at lower gain and bumped the R-09 up to the 13-17 range. I had been trying to keep the R-09 at around gain 10 before and sometimes had to turn it down below 8. I think that was eating up too much headroom in the external preamp.
Now I feel most comfortable in the 'teen' gain range zone and only use the line-in when using an external preamp, which is almost all the time. Nice to know I can switch over to the mic in without sonic compromise if the jack ever fails again, though.
No other reason to use the mic-in with an external preamp unless you need the additional gain - the noise performance is technically worse, but I never heard any difference at reasonable gain settings. I only use the mic-in on my second R-09 for plug-in powered mics without an external pre.
For reference- I'm typically going 4060>MMA6000>R-09 with the R-09 set to 13 (adjusting that if necessary once rolling, rarely) and the MMA6000 set around +10db, never more than +20db, and sometimes closer to +5db depending on the style of music and amplification level to peak between -12 and -6dbFS @24bit.