Mimaki has come a long way with Rasterlink. All new equipment will come with Rasterlink 6 and depending on the ink set that you choose...you'll have access to hundreds of profiles.
Since you mentioned 3rd party RIPs, that's probably the biggest downfall. Very slim on what's available for Onyx and even slimmer if you're leaning away from CMYKx2.
I worked for Mimaki when these products were released (JV150/300, CJV150/300) aligning one print head is much easier than two. So I have seen some complaints about quality being better on the 150, but it was strictly due to the capabilities of the technician that installs the machine.
Besides from the bulk ink, the 300 also features a larger post heater out front since it can print so much faster.
The pump tube feature is really cool as it fills the capping station from the bottom and you don't have to fuss with an eyedropper. However, there is no sensor to let you know when the cartridge is empty. So unless you stay on top of it, I have seen some machines that has the capping station feeding tube clog and the only option is to replace it if you want to continue using this feature. Stay on top of it and you'll be fine.
These new machines were built on the JV33 platform, so it's very well built and very well thought out.