The Ark also had to house Mainframe/Teletraan-1 as well as the robot mode having a passing resemblance to the Last Autobot. The Nemesis does have more creative freedom by no needing to house a secondary Transformer as well as having a completely original robot mode design.

It's pretty much also why Cybertron Primus is a better toy than Armada Unicron; because both Primus and Nemesis only need to resemble a pre-existing design in alt mode but with the liberty of completely original robot modes.

Plus coming later means that lessons learnt from their the preceding toy can be applied.