The ending was great, and generally I liked the style of it. But as you said, there's something not right with it, and it's throwing off the whole mix.
It sounds to me like a case of instrumentation - Sky Sanctuary's melody works especially well in the original because it's played strongly, with a hard synth. This arrangement using a softer and muddier lead shifts focus away from the melody, and instead brings out the guitar backing.
That's literally the only fault I have with it, so it's a 4. Keep up the awesome.