So basically we're allowed to have 5 skills in slot, and I feel like I sometimes want to have different variation of a same skill.
Skills very often serve completely different purpose depending on specialization. One straightforward example would be Javelin throw's Siege barrage and Divine Fury - One is more of a single target skill, while another is probably the famous "Javazon" Lightning fury AoE. Thing is, I love both variant and I would like to use javelin as my skill.
This sometimes gives me some frustration - because typically you end up with two active attacking skill anyway, and this combination is often fairly predetermined. Like If you're a throwing paladin that wants to use fury javelin, you're pretty much forced to also have hammer to cover your weakness, unless you're playing holy trail variant. I sometimes ask - why can't this secondary skill that i need to have anyway, be a siege barrage javelin?
I think this tends to make people specialize into more of a multi-purpose-ish nodes. Like holy trail can both serve as single target and AoE, Hammer skill itself is just multi purpose in general and hammerdin + smite is probably the most common variant, etc.
I think this happens to pretty much all the skills that specializes that skill into either extreme single target and/or AoE - like throwing stars vs Deadly Aim node on rouge's shurikens, specializing into any of those makes it unviable as a singular skill and it tends to make people look more into blade shield variant, which is also fairly "multi-purpose" that probably focuses more on single target, while chakrams are also fairly multi purpose that likely has better aoe clear than blade shield variant.
I personally see no problem (except for potentially weird interaction, like umbral blades might function weirdly due to how blade recall works?, or ~~ auras which don't stack, but might function weirdly if specializing it multiple times is allowed) letting players specializing a skill twice. A Multi-purpose skill that doesn't need two variants to function well will have another supporting skill to make it worthwhile, wheras if you decide to have two variant (mostly single target and aoe), you'll be able to focus on the skill you want to play. Potential balance issue, like much easier itemization could be counteracted with some penalties if you specialize same skill twice (like -2 max level, etc.)
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