25 carriages is quite long for a commuter train. Furthermore, assigning carriages for a specific stop is quite tedious and confusing to people.
I think it's practically impossible. Many stations, particularly the major ones, are heavily constrained by junctions nearby that simply can't be moved without extensive housing demolition, often involving expensive properties partly because they're fairly close to a major station. At central terminals particularly, the width of the railway widens considerably through the throat junction area on final approach to the platform ends. The throat areas have often become hemmed in by high value development, and there may be other constraints such as curvature or proximity to a major structure such as a tunnel or bridge. Widening and lengthening a throat significantly, even if possible at all, is likely to be extraordinarily difficult and expensive, not to mention highly disruptive during construction, and is still likely to lead to an end result of fewer, if longer, platforms. Longer trains would take longer to clear junctions, so margins between conflicting movements would also be increased, further decreasing train frequency capacity.
Double decker trains have a higher capacity than single level trains. Although the dwelling time would increase, the higher capacity would offset that. Since there would be higher capacity, less trains would be needed during peak hours, thus reducing congestion.
Equally double decking could theoretically add capacity for demand growth with the same frequency. DD could be confined to express first class saloons on longer hops as many Japanese suburban lines provide with their green class bi-levels on limited stop express routes. Green class passenger density is a little sparser than the peak standard crush at the doors and in the saloons concerned, so it may be by these means boarding times are not overly extended, and on the express schedules operated with the stock, the fewer stops mean their duration dominates the overall journey time equation to a lesser extent anyway, at least in comparison with the parallel all stations local trains which remain resolutely 100% single deck.
Japanese railways manage to squeeze these double deckers into a loading gauge on the 3ft 6in network that is, no doubt due to involvement of British railway expertise in early Victorian era developments, extremely similar to our UK standard gauge profile, including a high intrusive platform with similar clearances and requiring a marked car body side 'tumblehome' from it's widest extent at waist height to the narrower solebar level next to the platform edge. It should be noted however that Japanese railways, even with their complex platform signage and perhaps more orderly and undeniably typically shorter population only employ double decks for lower density niche applications such as green cars and a small number of long distance sleeper and cruise trains. The sleepers are dying out now due to continued expansion of the Shinkansen network however.
the latest Shinkansen expansions have been accomplished as 'Mini-Shinkansen' extensions over former narrow gauge rights of way retaining their more limited clearance, but gauge-converted to the Shinkansen's European standard gauge. Special smaller profile 'classic compatible' Shinkansen trains are procured to run over these extensions at a modest speed (albeit lifted considerably over former narrow gauge service) and to join and share the large profile trunk network running at full speed along with their larger 'captive' cousins.
DD on the full size Shinkansen was tried for a major series of trains in the 1990s but this feature has not been replicated in more recent orders, even though it is easily accommodated within the larger, squarer loading gauge more like the European and American carbody profiles. The DD E4 model with a rather limited top speed will soon be completely withdrawn as ticket sales have plateaued on certain busy commuter corridors, due to Tokyo property prices stabilising according to article linked below. Sheer seat capacity is now being traded for more speed improvements and route extensions.
http://ajw.asahi.com/article/behind_news/social_affairs/AJ201406060010
