Before I get started I should introduce interlining. Interlining is when two routes from separate trunk lines share tracks together, an example of which being the J/M lines along Broadway. While in most cases not severe, it does pose a problem depending on how problematic the merging is.
The 2/3/4/5 lines join each other in Brooklyn on the Eastern Parkway line. From Borough Hall to Franklin Av, the 2/3 run as locals alongside the express 4/5. East of Franklin Av, the 2/5 divert down Nostrand Av to Brooklyn College while the 3/4 terminate at New Lots Av and Utica Av respectively. However, the current setup poses a major problem. In order to get to President St, the 5 has to merge with both the 2 and the 3 before the formers merge away to Nostrand. This junction, known as Rogers Junction, is a severe bottleneck on the Eastern Parkway line and can cause train traffic and delays. It also limits capacity along the entire line.
But simply fixing it will not be easy. Given the junction's unique and complicated layout, rebuilding it would require eminent domain, and would potentially require Eastern Parkway to torn up in the area. President St and/or Nostrand Av would probably have to be demolished in order to allow for this complex rebuilding to take place, since the two stations directly abut the junction. Costs would also be astronomical. Knowing the MTA, they would probably declare this option automatically infeasible.
However, this is not the only approach we can take to approach the problem. If we swapped the 3 and 5 lines, so that the former goes to Flatbush while the latter goes to Utica/New Lots, there would be no merging whatsoever, simply eliminating the bottleneck. 2/3 trains would be able to have a service increase and could run together to Flatbush. 5 trains on the other hand would switch to local east of Franklin Av, stopping at Nostrand and Kingston Avs.
But since there's no merging, meaning extra capacity, this allows for the 5 train to be extended via Utica Av to the Kings Plaza Shopping Center in Marine Park. This extension has been on the minds of transit planners throughout the 20th Century and also to the present-day. It would serve a large transit desert in East Flatbush, which currently has no subway access. Bringing a subway line down there would be very beneficial to the local community. The 4 would then take over the New Lots line at all times.
Besides an extension down Utica, I've also highlighted potential expansions for the Nostrand and New Lots lines. One potential extension would bring the 2/3 from Flatbush all the way to Voorhies Av in Sheepshead Bay. This would be effective on relieving the B/Q, also serving a transit desert, but another thing it would also accomplish is giving the locals a more efficient terminal. The current layout at Flatbush Av is inefficient, mostly due to the fact that it's a side-platformed station and passengers have to know where the trains depart. Giving it a new terminal, would eliminate the present-day layout. Another extension that could be included is an extension of the 4 to Spring Creek. It should also be considered because Spring Creek/Starrett City are growing, and a new subway extension will eventually be necessary. It would simply involve extending the 4 from the present-day Livonia Yards and down Linwood St to Spring Creek.
Overall, deinterlining the junction will be very beneficial. The 5 would no longer have to merge with the locals, the 2/3 could run at an increased frequency, and it frees up capacity for expanding into underserved areas of Brooklyn. However, the only downside is that passengers will have to transfer across the platform at Nevins St and Franklin Av if they want either 7 Av or Lexington Av service. But ultimately, the positives outweigh the negatives and would be worth it.