It might be a good trade-up from a financial point of view, but personally I would not do it. If you spend the days speeding along on your Monster and trying to get your knee on the ground on every turn, the 999 might give you more power (and maybe handling) to play with. If you are like me and like to accelerate fast and go for the twisties, after which I can relax and ride comfortably, I would say stick with the Monster. I also think the monster is cooler and might actually be easier to trade or sell since the target group is bigger.
I am not smart enough to answer the 999 question, but what advantage would you gain going from a 2003 M1000sie to a 2004 M1000 dark (besides 1yr)? Would it not be a step down suspension wise, plus out 1500?
Way back when the real bikers had the 916 as their only transportation and girls were babes and hang a rounds, this swap could have worked. But not with the 999. The fuel tank is so small that the limited range will get you into trouble, and it is so small that you will have to refuel during a race. They now have an 18 liter fuel tank ready for the 749R so you have to get that one if you do the swap.
And how can you strap on some 30L of luggage on to the 999 tail piece, which you could with the 916? I can understand that you want the ultimate super bike, so why not look for a 916 / 998.
For the type of riding I do it would'nt be a good choice. Last summer I rode 10,300km from Toronto to Sante Fe and then up through the rockies through Co., Wy., Mo., into Alberta and back home to Toronto. I also commute 45min to work, so as much as I would probably love the performance of the 999 it simply would'nt be practical. I also don't know that I am a good enough rider to fully appreciate the ability of the 999 and I have more than enough fun on my 01 900 cromo. I would consider the multistrada although I hear you need an aftermarket saddle if you want to ride it any distance.