I'll start off with this, that was very nice, some awkward bits, but the styling of the background/foreground/characters really worked well with each-other.
The way that you handled the 3D models was pretty well thought out, I dig the cell shading.
I'm pretty sure a good deal of the character animation was directly rotoscoped, and sometimes the movement felt a bit off, but non the less still pretty impressive.
The BGM was an alright remix of the main R-type theme, not sure how much of that was in your control, but if so then I recommend having a prominent segment where the lead medley solos out at a higher pitch, and some more prominent synth backing would do wonders! (The arcade cabinet used a digital synth to make the music in the first place.)
The SFX were definitely above average, I understand the choice to mix in the arcade effects for this type of project, and it works.
Voice acting was a mixed bag, but hey that's Newgrounds for ya, everyone needs a launch point, and I never cringed, so I'd say it went pretty well.
So to sum things up, great job, and may you only improve from here!