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Mental, the size of the focusser depends on what you want to put in it. If you are visual only, the answer depends on what eyepieces you want to use.
The trouble with the smaller, short newtonians is that the secondary mirror becomes a visibly annoying big black blob if you use really low powers, and in this respect you need to keep the eye pupil well under 6mm.
I think anyone who would spent the $ for a 100° eyepiece won't be messing with a 6" f/5 scope, so I suggest its a fair bet that in this size of scope the eyepieces are likely to be fairly modest ones.
In a 6" f/5, I'd expect the longest focal length will be 20 - 30mm and midrange eyepieces will easily fit within the confines of a 1.25" focusser.
In either case (2" or 1.25") you must use a low-profile focusser to avoid vignetting the light cone.
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