Well firstly, your numbers are a bit out 
20*60*10 = 12,000 not 120,000! The wiki states that a full minecraft day will net you about 13050 EU.
In the name of science and being a nice guy, I loaded my 1.7.1 test world and set up 4 water mills, surrounded them with 27 water blocks and piped them to a batbox with tin cable. Using the EU meter is giving some really odd results like 0.02 EU/t over 14000 ticks. If I spam-click once a second I'm getting numbers like 60EU/t then 6EU/t then two lots of negative numbers! So I have no idea what the heck is going on there.
OK, I left the EU meter counting while I typed this post. 0.32 EU/t over ~20,000 ticks. huh?
The wiki goes on to suggest that water towers are "no longer working" but doesn't explain the manner in which they are no longer working.
I agree that water mills are cheaper and easier to get out there but the trade off is space and messing about with water buckets. You can easily cover the roof of your bunker with solar cells or find a nice stretch of desert and lay out a few hundred solars. To get a similar output from the watermills requires digging a bunch of holes then doing a lot of jumping around with buckets back and forth from your infinite spring.
There is a group that feels that solar are overpowered since they can't generate less than 1EU/t apparently. I guess the IC2 team feel similarly since a recent update switched them to requiring circuits instead of copper cable and also set that they didn't work during rain.
My problem is there isn't a middle ground in unattended energy production between the microvolt range (solar/water/wind) and the nuclear reactor. The generator and geotherm are both quite labour intensive and require regular feeding; something for which IC2 makes no provision. I did have a lot of fun setting up a MineFactory tree farm with RP2 taking the wood to IC2 furnaces and then to generators. Worked an absolute treat but sadly lagged out my SMP world for the other players so I had to can it 
I've made the following comparisons-
over the coarse of a 20 minute day, solar energy runs for 10 minutes. At 1 EU a tick, that works out to 20(ticks in a second)*60(seconds in a minute)*10, or 120000 eu a day, not taking into account the weather (raining? storm? sucks to be you).
over the coarse of a 20 minute day, water mill energy runs for 20 minutes. From 1 generator, you get 2 mills. Hands free, and with water in 25/27 possible locations, you have 0.25 eu a tick, working out to be 0.25*20*60*20, or 60000. But wait, you have another generator. Now, you're at 120000 eu a day, equal to that of solar, but without the awful weather problems. They are also stupidly cheap, compared to solar generators- 6 planks worth of wood compared to 2 circuits (a pain in the ass), 3 coal, and 3 glass. Who thought that was even remotely comparable?
Finally, you have wind power, which seems a lot more finicky than solar, but with potentially higher output. They seem like a complimentary power, that you add in addition to something else. Providing a boost to a steady stream of energy, and when they are generating sub optimally aren't going to screw you over. Is there somebody who has worked this out? I'd love to see how you/they have done it.
If I were to put all of my eggs in one basket, that basket would almost definitely be water power. But since the online guide suggests solar, I have 45 solar generators that I wish were water generators (an extra 90 water generators would nicely compliment my approximately 250 water generators already in place).
