Okay, well how long exactly are we talking about here to warm up? Give your starting and ending temperatures.
Also, has it occurred to you that eliminating the bypass might have something to do with this? I'm guessing the bypass is there to help speed up engine warm up times in addition to preventing a total blockage in the event of a heater core.
Pure water will conduct heat better than antifreeze (higher heat capacity), which will mean it will take the water longer to heat up than antifreeze. Either way, you should always maintain the proper antifreeze concentration (between 40-60%). You should check your concentration with a hydrometer. The system is not designed to be run with straight water, so that might have something to do with it.