I'm biased so take my opinion with a grain of salt. PyxelEdit fulfil all my needs, although they're not particularly demanding. ASEsprite is more feature rich, and is being updated more often as the developer is working full time. Danik is creating PyxelEdit in his sparetime, which means that updates comes less frequently.. or rarely currently.
The reasons i'm using PE instead of ASE is primarily because of the interface. The interface is more modern, and if you're familiar with photoshop or similar software, very easy to get into. PE lacks a lot of things if you compare it with ASE, but depending what you need or require, PE might be the right choice for you. PE is great for tile work and it's animation tool is intuitive and fresh IMO.
Short answer: ASEprite is very feature rich, and gets updated very often, but has a old and less familiar interface. PE is easy and fast to get into, is much less feature rich, has great tile and animation tools, a modern and familiar interface, but updates are seen rarely.
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