The Ju90 got a new fuselage since it was to be an airliner, an unnecessary change for a bomber, the relevant change is the new wing, and that could have been done as the Ju89 was developed and, seeing the V5 performance with the new wing, I really dont see the benefit.
The Ju89 needed major changes to the fuselage as well due to the low bomb load capacity, since it was only 1600kg, less than that of the He111. Unless you want to just mount bombs externally. The wing would also have to change and would the cockpit. The Ju290 was quite a bit different than the Ju90 in all the above areas.
As you can see, the new wing WORSENED the Ju90's performance, with more powerful engines (4x140PS) and slightly more fuel, max and cruise speed, and range went all down, same payload... so I dont see an improvement here, on the contrary.
So, in order to FIX that, it was morphed again into the Ju290, were the ungainly liner fuselage was enlarged yet again and so was the wing, and this ever growing mess needed 1560PS BMW 801s to drag itself across the sky...
I truly see no benefit to the Ju90/290 evolution, in the end the 290 needed 1750PS BMW 801s burning C3 in order to have a decent performance, I think with some development the Ju89 could have done much better and using readily available Jumo 211s at that.
Beyond that, heavy bombers are not maneuverable, not in any meaningful sense and they are slow to anyone trying to chase them down.
Of course the Ju90's changes made the military performance worse, because it was designed around civilian luxury transport needs. The engine used was only marginally more powerful until the Jumo 211F (a 1943 engine btw) or Double Wasp engines (American engines that weren't available in wartime) were added, but note that the empty weight went up substantially as did the loaded weight with passengers. Look at the max start weight too, that was quite a bit higher for the Double Wasp model vs. the Ju89. The civilian model was set up for something substantially different than the light loaded Ural Bomber design.
The Ju290 had to mount bombs externally, as the converted version was a military transport that was shoehorned into the long range recon role with bombs attached much like the Fw200 (it was adapted from the civilian version for the Japanese as a long range naval recon aircraft right before WW2 and ended up in the Luftwaffe when they were cut off from Japan).
The Ju89 had potential of sorts, but needed major redesigns to get there. A 189 using the experience and work on the Ju89 would have been just fine. The problem though is that Junkers, who designed it, was tapped to make a huge number of fast bombers, the Ju88, which absorbed their capacity to make aircraft especially given that they also made the Ju87. So they weren't really in a position to make a large four engine bomber. That's why the RLM went to Heinkel to make the Bomber A/He177 as a replacement for the aging He111, as it was intended to have excess capacity, while Dornier then made a 'heavy' multipurpose twin engine bomber, the 217.
As to maneuverability the Lancaster was actually pretty maneuverable and at night was agile enough to get out of the way of night fighters if it spotted them. The HE177 was also quite agile for it's size (even before the dive bombing requirement was added it was intended to be able to dive at a shallower angle), which meant easier handling in the air for the crew; not having that meant it would be much more exhausting for the crew to try and maintain and adjust in the air, especially during climbing and landing (nothing like stalling while trying to land), not to mention to get into formation and deal with unexpected situations where it would need to rapidly maneuver itself. Obviously it wasn't comparable to a single or twin engine aircraft in terms of maneuverability, but having the ability to be stable in the air when going through maneuvers was very important for any aircraft in combat at least according to Eric Brown, British test pilot who flew more aircraft over a longer period than maybe anyone else in history, including both British and German aircraft (he got to test out all the nifty Luftwaffe designs at the end of the war and wrote a book about it, "Wings of the Luftwaffe"). He even reported on the FW200, Ju290, and He177 and compared them to the British and American heavies. He does note that maneuverability in the air for heavy bombers isn't necessary so long as they have heavy defensive firepower to keep fighters off of them, which the militarized Ju290 did have. Apparently though the Ju290 did have better handling for rapid maneuvers to get into cloud cover in a tight spot than the Fw200 and even landed on a shorter strip than the 200.