I was curious in only the engine and transmission differences betweent he ES300 and ES330.

I was curious of the engine specs:
Bore
Stroke
Journal sizes on main and rods
Cyllinder Head valve sizes and flow numbers if possible
Are the intake manifolds the same
Camshaft specs ( are they the same )

And is the transmission upgraded.

Is the engine for the ES330 a completely different engine or is it the same as the ES300 with more stroke and bore? Do any engine parts interchange between the two? What about ECU's?

The newer 3.3L is based on the 3.0 from what I understand but they fixed a few things. New knock sensor system is probably the biggest upgrade, I believe.

I've read the engine is significantly heavier, though? Here's some links to help you out:

Toyota 1MZ-FE 3.0L - https://www.motorreviewer.com/engine.php?engine_id=149
Toyota 3MZ-FE 3.3L - https://www.motorreviewer.com/engine.php?engine_id=150

I really like my ES 300. I have owned a total of three vehicles with the 3.0 L motor and I really like it, overall.

I only feed them premium fuel and never have an issue with a knock sensor. They rev nicely and I think they put out good "enough" power. It's not enough to WOW you, but it's plenty to get moving on the highway with no issue.

Edit: will add some details -
'04 Avalon with the 3.0L had 247k on it when I sold it, engine ran perfect, no consumption what-so-ever.
'99 RX 300 - 211k or so on it now, runs perfect no consumption issues
'03 ES 300 - only has 137k on it so not a big deal, but also runs perfect.

Great engine, I love them.