BowTie2 (gapped aligner for RNA-Seq reads)

I always wondered why short read aligners were not increasing the length of alignable reads given the fact that sequencing technologies are pushing harder day by day to improve the read lengths. Current ultra high-througput machine is TruSeq (from Illumina) that can generate read lengths of 100X100 bp (paired).
BowTie has been traditional short read aligner since it was published in GenomeBiology in 2009 but was unable to performs gapped alignments of long reads. Recently, on October 16, 2011, new version of BowTie (BowTie2) was released that can perform gapped alignments. I haven't started using it but will soon will. Hopefully it will alleviate the slow speed problem in long read alignment such as using BLAT.
BowTie has been the core alignment tool for several popular RNA-Seq pipelines such as Trans-ABySS, TopHat etc. Does the release of new BowTie version affect those pipelines as well?
Will keep you posted if I find anything interesting related to BowTie2.
Thanks for reading.