My two penn'orth worth.
Firstly suspension is a very personal thing as everyone will 'feel' something different. I also think the various ages and types of suspension fitted to Monsters over the years adds another dimension to this 'feel'.
The standard set-up on any motorcycle will always be a compromise as the manufacturers need to cater for all shapes and sizes so having the correct suspension spring weights for your own weight (remember to add that of your riding kit) will be the biggest thing you will notice, particularly if you are at the ends of the 'average' spectrum i.e. like Danny Pedrosa or Yamamotoyama.
Moving on from this if you have never touched the suspension, changed the fork oil etc. and your motorcycle has either covered a big mileage or is knocking on a bit then again, you will notice the change a refresh will make.
Quite rightly, the suspension does need to work in harmony so changing the rear will almost certainly make the front feel worse (although overall, riding the bike may well still feel better if that makes sense?).
As Nick has mentioned referencing his 748 'magic carpet ride' comparison, is that the earlier bikes (up to the 6/796/1100 on I would say) are inherently quite 'flighty' when pushing on a bit down bumpy B roads and the like because their suspension is quite basic.
The standard (certainly Marzocchi) forks, have too much compression damping over small movements making them kick off bumps under acceleration, but not enough compression to support them over large movements such as hard braking. Couple that with not enough rebound damping making them 'pogo' when you release the brake and a spring that is too stiff for most rider weights means there is a lot that can be improved upon.
Starting off with Showa forks gives you more options and I cannot really comment on those other than to say that personally I am a big fan of Maxton's customer service and the improvements their cartridge conversion made for me. You can go around a lot of houses spending a lot of money and still not be a whole lot better off, so going to a well respected suspension company/specialist will be a lot cheaper with a greater (and quicker) reward in the long run.
As for the rear shock, again I can only comment on the original fitted to my 1997 900 which never really felt nice compared to that of my Suzuki GSX-R750WT which I owned at the same time. The shock was eventually changed at about 8000 miles in 2005 (my mate who bought my Monster new only put 800 miles on it in two and a half years or so) for Nitron's NTR R1 (Sport as it was known back then) which has quite simply been brilliant over the last 25,000 plus miles.
It went back for it's latest service a couple of years ago, came back like new with a new spring fitted as I'd put on a little weight- (middle age spread) and my bike has never been better to ride as a result and I love it more than ever.
However after all that, by comparison my 12,000 mile 1996 Yamaha Thundercat still on it's standard original suspension (fork oil changed and linkages stripped and greased etc. recently mind) along with it's extra 20 (or so) Kgs. is still a much more composed ride down a bumpy road though.
The last thing to consider is probably cost versus how long you intend to keep your Monster- quality work costs but if it's a keeper then do it, if you get it done right you will not regret it.
