Depends on what you want to do and how long you want to keep your bike for. The advantage of bigger bore bikes is that you don't sustain high revs at hi way speeds over longer distances, so less wear and tear on the engine over time. A small engine is going to suffer more riding at high rpm for long periods of time than a big bore engine at lower rpm. That's why so many 5/600 ' s are beat to crap after 30,000km while 1000 CC's and above can go 100/200,000 km no problem...
I wouldn't count on that being the case. Decades ago, people said the same thing about those tiny fast-spinning aluminum Honda car engines - that they wouldn't last as long as their tried-and-true Chevy big block V8. Look how that turned out.
I know of a '99 Yamaha R6 with just short of 100,000 km on it. I know of a cbr125 which had (I think) around 65,000 km on it when the owner sold it. I know of a Ninja 250 that has over 80,000 km on it (and it is someone who participated in this thread). I know of an EX500 with 110,000 km on it. My Fizzer 400 is "total mileage unknown" but it had at least 50,000 km plus 3 roadracing seasons for the previous owner when I had it apart to freshen it up and fix a known Yamaha OEM assembly flaw. And that brings up the real issue ...
Neglect, abuse, weak points in the design, and sometimes just plain bad luck are much greater factors for how long these engines will last, than what the displacement is.
Honda had issues with high oil consumption on some cbr1000 engines, but the 600s have been bulletproof except for those infernal timing chain tensioners.
Yamaha not bothering to screw in a pair of oil-restrictor jets all the way into the bottom of the threads has prematurely taken out many crankshafts and con-rods on FZR400 and FZR250 engines. (It generally lasted longer than the warranty ...) Unfortunately, the only way to inspect and correct this fault so that it never happens again is to take the engine *completely* apart.
I had my 2004 ZX10R engine apart to replace a pair of thrust washers that they made of the wrong material. (They fixed this for 2005) The engine was practically new-looking inside, at 70,000 km, except for those thrust washers. If one of those thrust washers lets go, the alternator rotor contacts the stator and throws magnetic metal shrapnel all over the inside of the engine.
None of these are displacement-related ... they're just things that for whatever reason, the manufacturer did not get sorted out prior to production - and in some cases, never bothered to fix ...
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