Congratulations on the new purchase. I'm glad you posted the question as I'm in the same situation. For me the RT-S is the spec I'd like, prefer the darker wheels and it has the running boards etc. The question is compounded in the UK because we only get the rts in white or cognac. My preference is black. The base rt is available in se6, but only in black.
I'm firmly in the '14 camp for many reasons and am seriously considering the base model. In the UK the foglamps and leds the rts should have didn't make it for homologation reasons. Conversely, the base rt gets the same glass headlamps that the fogs go in, so aside from the dark components the differences in spec between rt and s are;
rider footboards
front trunk lining and light
heated passenger grips
Adjustable rear shock unit (same shock though)
normal fenders as opposed to refined fenders
secondary gauges
the difference in price is £3500 which is I guess like $6k. Of the above, i think footboards and trunk lining are the only must haves for us, the new fenders do look nice but I can live without them. This gets me my preferred colour, all else I can sort over time.
I'm not sure I agree on resale value, over here the Spyder is dear, the lower price point of the RT and the better value it represents I don't think the S will sell for £3.5k more than its equivalent age/mileage RT counterpart. As said already, the RT already has a generous package, its only putting them side by side through brochures etc that you notice the differences. To a used buyer an rt is an rt, it has stereo. check, adjustable windshield check the rest comes down to if you want dark wheels or chrome as the remainder is negligible imho and can be added.
I also like that the base RT gets other black plastics, on the windshield and panniers, it has black panels, instead of the aluminium coloured highlights which the S gets. If I could get the S in black it would have made it easy for me and saved me hassle of powder coating parts later, but as things stand, we're thinking the base RT at the moment with addition of possibly rider footboards and frunk liner!
The alternative was an RTS and respray it Scandal green but for the extra outlay including the spray, I'm struggling to justify what is already an expensive purchase.
cheers
Nito