100% Savage....  I haven't owned a Rebel, but I have ridden and worked on a couple...
The Rebel is anemic at highway speeds,(low 70's mph with no headwinds)... the Savage is just minimally adequate, but,... it is adequate(88mph...at least 80mph uphill with a headwind)...  
... and the Rebel has valves like toothpicks... I've seen some bent ones, and they look like you could bend them with your thumb...
It's a great beginner bike, and mpg commuter,... but, the Savage has 4 times the grunt... very capable on the highway, but not a distance highway cruiser,...
it prefers to enjoy the scenery... ...

Do a very simple "spark plug door" mod, and change the petcock to a Raptor ($30.00),... and the Savage is a maintenance dream...

If you feel you need more than that,... I'd recommend going to a 650 DP bike for maximum power with easier maintenance than your Ninja...  
Look for Screw adjustable valves (not bucket and shim) and air-cooling for easiest maintenance...
Hydraulic valves would be easiest, but I don't know of an air-cooled single with hydraulic valves...

Harley Sportsters have hydraulic valves, single carb, and air-cooling, but are way overweight (200lbs more than a Savage, and top heavy) and tend to be unreliable...

I have owned both. Prior to my S-40 purchase last July, I owned and rode the Rebel for almost 2 years. Great beginner bike. Never left me stranded. Would recommend for a beginner.

Now for the S-40.  More zip,  better handling in the wind. Handles the hills better and I love the cornering this bike can do.

Drawback vs Rebel.. No dipstick, speedometer is on tank and not on handlebars. no trip meter. But then again more zip. I loved my Rebel but am in love with my S-40...

The S-40 allows me to keep up with hubby more as he doesn't call me "pokey" as often now..

I have an S40 and a 2007 Ninja 250. I have not had a 250 Rebel. I suspect you will find either the S40 or the Rebel somewhat of a disappointment after the Ninja. Valve adjustment on the Ninja is a pain, but valve adjustment on the S40 is no pleasure either. Battery replacement on the Ninja is easier. Oil and filter change is a wash. The S40 calls for retorquing the head bolts every 4000 miles, and depending on tolerances on the frame and engine this might call for removal of the engine (if you do it - few do). The brakes on the Ninja are much better. Fuel range on the Ninja nears 200 miles - the S40 is about 100 miles per tank. If you like a tach, forget either the S40 or the Rebel. Suspension on the S40 is harsh. The speedometer on the S40 is on the fuel tank, which means you have to look further down to check it, and a tank bag will cover it up anyway. The S40 has no trip meter.

With those comments, I do enjoy riding the S40. I have taken it for a couple of fairly long rides (400 mile days) and it does just fine. You do have to keep an eye on your fuel state. There are some parts of Nebraska where fuel stops are widely spaced. I have not yet ridden the Ninja that far in one day, but I will comment that the engine on the Ninja is considerably smoother.

I started on a Reb250 and moved up to the savage as an easy step up. Savage is only about 40lbs heavier. I wish Id just started on the savage. Rebel is too weak for extended highway riding. The savage can at least keep up with all legal speeds and then some. Gas mileage isnt as good but its pretty close and the savage is more fun. They can both be had used for similar prices.

I also meant to add that IMHO you don't need to do any mods at all to an S40 unless you just like to tinker.  It is a fine bike in showroom, stock form.

Mine has a windshield, and I wouldn't do without one, but that's not really a mod to me.  Mine also has a Sportster muffler put on by the previous owner, but as soon as I can find my OEM muff, in my basement with piles of other stuff, it's going back on.  I don't really like the loudness of the Sportster muff.

Anyone ever screw up, leaving a stop sign & seeing something coming, closer, faster than you thought? Thats when having a bike that has some Punch can really be a good thing. Or, you can just make sure you never screw up..

Love my S40 and agree with all the comments above.  
But no one mentioned the best advantage...  SuzukiSavage.com!  The Rebel may have a forum too, but you won't find a better group of supportive people than right here!!

Other bikes... The Eliminator is a Kawasaki, right?  I think its 250.  And I believe Kawi also makes a 500, or at least did, the Vulcan 500, I think its nice.