I'm a heavy Aperture user and quite happy with it. I tried Lightroom back when it was only a beta ... so it's not fair to compare that functionality to Aperture. Today, I have friends who use Lightroom, and every so often we discuss features. I've learned that it has a few features I wish I had, as well I have a few features they wish they had. I'm not really certain who's ahead w.r.t. features or performance, etc. but Lightroom is probably ahead based on market share.
I think Lightroom 3 was behind in features, but now that they've released Lightroom 4 it seems most of the functionality Aperture had over Lightroom is finally in Lightroom as well (I'm not sure about file management though... the friends I have you use Lightroom don't think they can do some of the things I can do w.r.t. management of offline (aka "referenced masters") images. But it's also possible it does something in that area and my friends have never tried to use it.
Either way, both are really optimized for a RAW workflow and you'll get the most out of them if you shoot in RAW (both can handle JPEGs as well.) Both let you edit images in Photoshop if you need to do something they can't do natively. Both have plug-ins.
You'll find that they can both do about 95%+ of everything you'd ever want to do with an image. I hardly ever have to invoke Photoshop to do an edit, but I guarantee you will occasionally still need it -- particularly where heavy manipulation is required (Aperture & Lightroom are mostly intended to do "adjustments"... not heavy manipulations.) Their major advantage is that they are a combination of a non-destructive RAW workflow and imaging adjustment app AND a digital asset management app at the same time. So you import entire shoots and the "adjustments" you perform can be performed on the entire shoot all at once (you can sort-of do that with Photoshop but it's more cumbersome... you don't actually open & save files in Aperture or Lightroom like you do with Photoshop.)
I definitely recommend you own one of these two.
As for filters:
ND filters change your shooting conditions by cutting light. If you need a slower shutter speed or a wider aperture than the lighting will allow, the ND filter will cut the light so you can do that. Other than that, the exposed image should look the same (noting that a wider aperture will narrow your DoF so it can allow you to blur the background and a slower shutter can help you imply motion into your images -- but colors, saturation, contrast, etc.... none of that will change with an ND filter (at least... let's HOPE not.))
As for circular polarizers... I HIGHLY recommend them. It's one of those things that should be in every photographer's bag. By selectively allowing light to pass through the filter based on the polarity of the wave it has the ability to cut reflections... but that's just the beginning. The side-effect of cutting reflections is that there are micro reflections in everything... the waxy coating on foliage, the droplets of water vapor in the air, etc. Consequently not only can you shoot subjects through windows a lot easier, you also get richer color saturation when shooting outdoors. Skies are bluer, plants are greener, clouds pop more, etc. Just be aware that what the filter is _really_ doing is based on light polarity, so angle of reflection will have much to do with how well the filter works.
A good filter (regardless of ND or CPL) should block light evenly. Some poor filters block certain wavelengths more than others resulting in a color cast. You wouldn't want an ND that, in addition to reducing light, also makes everything look greenish... or pinkish, etc. the color should remain the same... but merely get darker. But some will put a color cast on your images. Same is true of CPLs.
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