If I had to choose between 1 - 2.5" line and 3 - 1.5" lines, I would probably choose the later since I would have some control over each line that way. 3 - 2" lines would be even beter but make sure the lines are dedicated to each suction port (i.e. not shared) and they go all the way back to a large header at the pad. For three lines, a 2.5" header should be used although you could get away with 2" since the pump, heater and filter are all probably 2" anyway.

Shorter turnovers are not that bad but if I had my choice, I would design the pool with longer turnovers/run times. Skimming, chemical distribution and filter all seem to work better with longer run times and lower flow rates. So to save money, it is best to design with longer turnovers.

Ideally, I would design for the low speed of the pump for a 12 hour turnover so I could run at low speed 24/7 and still have 2 turnovers. Also, that would allow for up to 4 turnovers a day at high speed if you really needed it.

However, with 13k gallons you only need 18 GPM for a 12 hour turnover. Even with the lowest HP pump available at low speed, you will still have much more than that. However, the Intelliflow may be able to get that low and you could still use it for the spa with multiple strengths for jets. Even though it does cost a lot, it may be your best choice as it has the most flexibility and allows you to get away with a single pump for your entire pool and spa.