In his defense, there is a legit psychological phenomenon (which sometimes glitches or generally doesn’t work, so it doesn’t always apply) where you can’t find someone attractive if you grew up with them.  
And Spike’s seen Twilight pretty much for most of the day ever since he hatched.  
So, of course Twilight’s the least sexy mare in Ponyville; As far as his brain’s concerned, she must be a very weird-looking sibling (or other family, but their ages are pretty close, I think the instincts would assume sibling)  
In actuality she’s his Guardian, and he’s her Ward, which is such a vague and varied relationship it’s entirely a toss-up how the two think of each other. But she does seem to love him less than Shining, but more than anyone else.

@Background Pony #1A3B  
“…you put paint on your eyes?”  

“I was painting your bed gold as a surprise for you…”
 
The Hell?

Apparently, its possible to paint pony eyes

Awkward as fuck