I just bought an '06 Tundra Access Cab with V6 and 6-speed. The tranny is very easy to operate, although the throw is long and the clutch pedal is stiff compared to a car. Of course, the last cars I owned with manuals were both Miatas so perhaps that's not a fair comparison.
I would have bought a manual Yaris when I bought mine, had they had any in decent colors, but I'm increasingly glad I didn't given how many people on Yaris forums complain about the gear box on them. The powerband of that little 1.5L is stretched pretty thin over 4 ratios (not that it's going be much of a puller no matter what) but little that I've heard makes me feel like I'm missing out on an expecially engaging drive because of my auto. Besides, you can still force a downshift for passing or the twisties in the auto.
I haven't driven the Automatic, but I have clocked 35,000km on the manual. Initial clutch take-up was a bit finicky when new and it was easy to stall the thing, but after the clutch got some wear and tear on it, take-up was ok. Still not as good as my old Civic (but that car had a bigger engine and more low end torque while weighing the same as the Yaris). But once you get going, the DOHC engine in the Yaris really shines through. You can make some serious tracks on the road, while keeping the rev's in the 3k to 5k range and still get good gas mileage.
It'd be cool if the Yaris had enough initial power to make for easy clutch takeup. e.g. In my old 98 Civic Hatch, I was able to easily take off, with my foot off the gas pedal, even on a slight incline...it had that much low end grunt.
I know this is an old post but drove a 07 yaris today with the auto and I was d*mn inpressed! This thing had plenty of power, not a bad or noisy ride either for a small car. I was trying to sell my Tundra and get a new one but a 50 cents jump in gas made me rethink it again since my 2000 runs like new with 107k and is paid for I just ran some figures and my me driving 2000 miles a month is costing me 357 a month in the Tundra where the Yaris would cost me 147 a month. My payments would be around 160 per month and I could park the Tundra and use it for work only instead of all the time. I figured over 5 years the difference in gas to be over 12k at todays gas prices. The one I drove was on special for 12,900 but it was a hatchback and I really liked the 4 door sedan better and it looked better to but trying to stay on budget so I'm undecided yet.
I found my first dislike in some of the new manual trannies. I drove an '07 Camry, '07 Altima, and '07 Sonata and all exhibited the same trait. The drive by wire system does not like quick shifts from what I can tell. By taking your foot off the gas between shifts it reacts too slow when you step on it again. Just like some complain on the Tundra and Sequoia about not getting full throttle from a start. It makes me feel like a crappy stick driver because you rev it out some, shift and step on gas again and it actually slows down for a second.
I ended up getting a new Sonata 4cyl, 5 speed stick because for $16,600 out the door it can't be beat. ABS, Traction control, Stability control, 4 wheel disc, PW, PL, tilt, cruise, A/C, side impact air bags, front and rear curtain bags, normal driver and passenger bags, CD player with MP3, cabin filter, HUGE trunk, more back seat room than the Camry, AND 34 mpg highway while having plenty of room for my family.
Now I just need to improve the power delay when shifting somehow.
I test drove an 07 VW GTI with DSG (dual-clutch) over the weekend, and while I loved the technology, I still longed to shift. Even with the game console-like paddles I wasn't fulfilled. However, in driving larger vehicles (especially trucks), I always prefer an auto. For me, cars are to be driven and trucks get you from A to B. If you get a Yaris, definitely go with the manual...it will make the 1.5l much more enjoyable. If you get a truck, get an auto and cruise...
I use to by stick shifts when my children were young now all are married. Only one, my youngest daughter ever purchased a standard shift vehicle. I sometime get tired of driving and would like someone else to drive. Some people say they can drive a manual shift vehicle. Very few really know what they are doing. Riding the clutch dumping the clutch. This variable speed automatic in my Yaris is the smoothest tranny I've come across... If I knew I'd be the only one driving my yaris I'd say stick but I've seen to many people go in to a hilly area and not know how to hold a car on a steep grade until you can move again........auto for me and only 1 mpg difference. God can't always be your copilot.
Automatics typ are MORE efficient on the highway with a stick due to LESS mechanical losses thru the drivetrain with a lockup converter (yes I said automatic) though i hear the CVT can be LESS efficient due to high hydraulic pressure required to maintain the "pully" width. Recall that manual tranny's have all gears in constant meash and are often lubed with 85W gear lube (sim to a 40W motor oil - the weights dont directly translate across motor to lube oils) and tend to generate heat in OD gear and thus less efficiency.
Me, i like to shift - especially in my 07 Chevy WT 4.3L V6 pseudo "Craftsman Truck" If you havent driven a '67 427 BB impala with 4 speed Muncie, headers dual cherry bombs and posi rear end, you ain't lived, boy.
- Grumpy in NH
35 years NIASE Master Tech/ Race Mechanic
Automatics typ are MORE efficient on the highway with a stick due to LESS mechanical losses thru the drivetrain with a lockup converter (yes I said automatic) ........ Recall that manual tranny's have all gears in constant meash and are often lubed with 85W gear lube (sim to a 40W motor oil - the weights dont directly translate across motor to lube oils) and tend to generate heat in OD gear and thus less efficiency.
Incorrect.
Take Yaris as example:
5-speed manual is 21.7MPH/1000RPM (top gear) , 75W-90 (most likely dino) and 34/40 MPG.
4-speed auto is 22.2MPH, WS ATF (synthetic) and 34/39 MPH.
How can auto model rev less on highway (TQ lockup) with synthetic fluid but produce less MPG?
Re: Auto vs. stick, your opinion.
I just ran some figures and my me driving 2000 miles a month is costing me 357 a month in the Tundra where the Yaris would cost me 147 a month. My payments would be around 160 per month and I could park the Tundra and use it for work only instead of all the time. I figured over 5 years the difference in gas to be over 12k 
at todays gas prices. The one I drove was on special for 12,900 but it was a hatchback and I really liked the 4 door sedan better and it looked better to but trying to stay on budget so I'm undecided yet.
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