I struggle with incorporating all of these elements as well while training for football. I share your concern that the second SVS workout (from the Arthur book) is too stressful on the CNS over the long term.
I think there are a couple of ways of approaching this. One thing to consider is that if you are doing team practices, then much of your agility work may be covered by that in a very sports specific manner (actually playing your sport!) In that case, simply doing some quality speed and acceleration sessions, (1/week ea) may be enough.
On the other hand, if you are on your own in GPP or SPP, then things may change a bit. First off, by your own description, your sport “involves mostly agility and short accelerations.”
If that is the case, and you are following a short to long program, it probably makes sense to develop acceleration first in GPP, with a smooth transition to speed early in SPP and then keep that in maintenance (1x week maybe?) during late SPP while you focus your CNS energy back on acceleration and agility (which is the requirement of your sport - LaX?)
Actually, could you even make an argument to not train speed, just acceleration? We certainly can avoid SpEnd. If so, rotation of training modalities would have to occur more often to avoid plateaus.
Personally, after I get out of the early stages of GPP, I like to keep all of my high intensity elements on the same day with a day of rest between them.
So you could do:
M: accel, plyos, weights
Tu: tempo
W: agility, plyos, weights
Th: tempo
F: speed, plyos, weights
Note that depending on how long you take out the accelerations on Monday, this workout could have a bit of a speed component as well. Likewise, agility work usually heavily involves short accelerations.
Or if you want to combine things, something like:
M: accel, speed, plyos, weights
Tu: tempo
W: agility, accel, plyos, weights
Th: tempo
F: agility, speed, plyos, weights
would give you two sessions of accel, speed and agility each week, but that is a lot of different activites to fit into a single session.
Don’t know if this was any help or not? Thoughts?