Yes, it has been confirmed that the new anime series of Rurouni Kenshin will be a remake of the classic Shin Kyoto Hen (New Kyoto Arc), in which Kenshin ultimately fought Makoto Shishio. The only difference is that it will be told from Misao's perspective O.o.
If anything, this is not a exact remake, but a Rewrite a la Death Note.
Original RuroKen anime director Kazuhiro Furuhashi is directing the animation at Studio Deen, the studio which produced the RuroKen motion picture and OVAs. The first of the two new OVA episodes will premiere theatrically this December. The 1996 TV series voice cast will reprise their roles with the exception of Ken Narita who will play Hajime Saito in place of original voice actor Hirotaka Suzuoki.
Source: ANN