I believe the Ninja is going to be smaller, if it's the 68/4500 I'm thinking of it's only about an inch longer then they're 45/4500; it's insanely small. Also, it's the ultralite reg which is more expensive then the regular ninja. As far as the crossfire, perhaps a combination of the UL Ninja reg and the fact Crossfire now makes their tank cylinders in house so they don't have to pay an outside company.
And tank covers, that's up to you. If you get a ninja tank, just get a ninja cover from them all in one shot. Otherwise just look around, I usually buy an older version tank cover from websites that didn't sell the previous year or two models, saves some money.