Why has it been difficult to establish a phylogenetic classification
for bacteria?  Will recent technology make this type of classification
more likely?

See http://www.bact.wisc.edu/Bact303/Phylogeny

Bacteria are capable of horizontal gene transfer. This can make
contructing phylogenies difficult. TIGR (http://www.tigr.org/tol/)is
currently sequencing the genomes of different bacteria. The data
obtained should make determining evolutionary relationships easier.