EVE Online is no exception. The current trees for ship progression and skill advancement are the result of numerous patches, additions, and alterations to a core system that's left an enormous mess behind. As a result, the whole system is in need of an overhaul, one that the most recent development blog discusses in detail.
The first changes involve cleaning up and streamlining the progression system so that ships such as Destroyers and Battlecruisers are a part of the standard path rather than unusual deviations. There's also a removal of some of the more labyrinthine requirements for tech 2 ships. The other major focus is a removal of the current system of ship tiers, with the developers trying to specialize ships based on roles and make each hull useful in its own fashion. EVE Online players are going to be seeing a big upheaval in the way that ships work in the future, so it's probably a good idea to get a feel for where the changes are arriving sooner rather than later.