Firstly, on nozzle size, the most height you can lay down in a layer is in direct proportion to your nozzle size. So a bigger nozzle can do a slightly larger layer height than a smaller nozzle. This means faster prints as the nozzle can lay down taller layers. Generally though most people will go for smaller layers to give a higher print quality. So in such cases a smaller nozzle is better because it also puts out a narrower extrusion which means thinner, more accurate walls.
0.35mm are really the standard in nozzle size. Pretty much everyone has moved to this size with 0.5 being the old standard. Smaller than 0.35 tends to produce more issues like jams. In fact if you are going to try some of the more experimental filaments like wood, a 0.5 nozzle is better because it will get less jams from oversized particulates.
JHead and Makergear are good hotends. Makerbot are not ... in fact everything Makerbot produces is ok but not great. If you want the greatest flexibility you should look at the Arcol or soon to be released Prusa hotends. These hotends do not use a PEEK insulator so they can go over 250 degrees Celsius. This opens up materials like PP3DP/UP filament, polycarbonate, nylon, PTFE and PEEK as you can easily go to 300C with both. These are also great hotends but discussed less regularly because they are more expensive and a little less readily available (Prusa's hotend isn't even out yet http://prusanozzle.org/
). The Makerbot hotends now use PEEK/PTFE free design too but the barrel is too short and I find it has more overheating (heat getting up into the extruder body and premelting filament causing a jam) issues that Arcol (or Prusa is likely too based on posts/claims Josef has made).
Budaschnozzle is also a solid choice but it is based on an older Arcol design and reintroduces PEEK so it has the same max temp limitations of JHead and Makergear hotens. If you are going to pay that much buy a real Arcol.
If your choice is between Makergear and JHead, choose the Jhead - it's easier to assemble and repair if something goes wrong.