While the Nighthawk is a decent motorcycle for what it is and what it costs, it is an older design and it is definitely at a technological disadvantage compared to the little Ninja. The Ninja has a better chassis, suspension, engine, and transmission. All of these things, plus steering geometry (rake, trail, wheelbase, etc) designed for more precise handling should all contribute to a better overall experience. Really, despite its small displacement and the lack or respect from the Squid crowd, the 250R is truly a fine machine for the money, particularly the new ’08.
And, while (in my experience) the MSF bikes are remarkably well maintained for what they go through, there is always the chance that the one you rode was suffering a little from a relatively hard life. Oh, and I generally hated the transmission on the last Nighthawk I rode; shifting was a little hit or miss and finding neutral was like trying to find Atlantis.