Those who have already used TX a few times have probably figured out much of what they need to know to utilize it best for their particular needs. How best to use it, of course, depends on where your actual destination is and how often and when you want to ride it. Those going to places in Tokyo other than Akihabara and Asakusa may find that transferring at Kita Senju saves you time and money. Particularly if you are going some place in Tokyo that is served by the Chiyoda or Hibiya subway lines (or that you can easily transfer from these lines to others), Kita Senju is definitely the place to transfer.
When returning at peak times, you might not be able to get a seat at Kita Senju immediately, but as many people get off along the way, you shouldn't have to stand very long. If you have a train schedule with you, just add 11 minutes to the Akihabara departure time to get the times trains leave from Kita Senju. The route to the TX station out of the subway lines is not very well marked yet, but it's not difficult. You just turn to the left coming out of the wickets and left at the first passageway, up the elevator to the top and both the JR Joban and TX entrances are right in front of you (along with the Tobu Isesaki Line).
If you are going to places to the northwest of downtown (such as Ikebukuro) on JR, then it is definitely quicker to transfer to the Joban at Kita Senju and then transfer to the Yamanote or Keihin Tohoku lines at Nippori. As the Akihabara Station is very deep underground, you need about 7 minutes just to get out of the TX station and up to the JR tracks. If you are going from Tokyo Station on the Shinkansen, it will usually be a bit faster to go to Akihabara anyway (as there is only one transfer instead of two), but it will cost you an extra 150 yen, since your JR ticket is the same from either Akihabara or Kita Senju.
When we all used the highway bus before TX opened, we could get "kaisuken" and get a discount. You basically had one free trip for every 5 you took, and so it was a good deal. The TX "kaisuken", however are not nearly as attractive. You have to by a set of 11 for the price of 10, and as they are to a specific station, it makes it hard to use them for other stations. For instance, if you get a set to Kita Senju, if you want to use it to go to or from Akihabara, it is not just a matter of paying the difference of 150 yen. You have to buy a separate ticket from Akihabara to Kita Senju, which is 280 yen. On top of that, unlike the bus tickets, the TX tickets have an expiration day only 90 days after you get the set. If you don't use them, you loose them. Thus, you need to be a fairly frequent user or be able to share the tickets with others to make it worth your while. If you plan to go in frequently on weekends and holidays, you can get a bigger discount on "kaisuken" that are limited to use on such off time periods. These come in 2 forms, one that is also good on weekdays between 10 am and 4 pm, and the larger discount (28.6%) for those limited to weekends and holidays. Of course, regular commuter and student passes are available and a significant discount, but even these are not nearly as discounted as similar passes on the Joban.
So, do a few trial runs to check out what works best for you. Remember also that the highway busses are still available, and you can utilize those from Tokyo Station on the way back if it's convenient for you. And for those living in or around Namiki, the bus is convenient for getting back. Needless to say, few people ride the busses into Tokyo, but quite a few still take them back. One wonders how long this service will continue to last. At a minimum, they will be forced to reduce the number of buses.
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