Hola! We decided on a new order (our initial plan) versus backtracking from Barcelona to Ibiza back to Barcelona.
• 3 days: Amsterdam/Netherlands
• 2 days: Paris, France (easy 3.5 hours train ride on Thalys from Amsterdam)
• 3 days : Barcelona, Spain
• 3 to 4 days: Rome/Venice, Italy
• 3 days: Prague, Czech Republic
• 3 days: Berlin, Germany
•* 2 days: Amsterdam/Netherlands OR just fly out of Berlin
*We’ll end our trip in Germany or back in Amsterdam at our friend’s place...more than likely we will depart from Berlin though.

Will sort it all out this weekend and then take a breather. I know my brain is super fried at this point lol

If you are looking for a nearby alternative to Rotterdam, I like Utrecht though it might suffer from richiavo's criticism of being a mini Amsterdam - however in my view it has more to offer than Delft. However public transport is so good I wouldn't worry too much where you stayed you can easily get wherever you want to go . See www.9292.nl.

"Thanks for your reply can you also list the must see places as per your itinerary".
It's YOUR itinerary, non MINE.
There are tons of so called "must see places" between Nuremberg, Amsterdam, Paris, "Switzerland" and FRA.
But in 2 weeks, you will have no time to visit more than those you mentioned.

Who needs a cruise? Apart from Sado Island, I've been to all of those ports anyway.

I was thinking about this for a European "river cruise" up or down the Rhine-Main-Danube. Why pay over $1000 per day for a bed and meals? Just catch trains to all the desirable riverside (ish) cities all along the way from Amsterdam to the Black Sea!

Find any cruise ship with this: https://www.cruisemapper.com/?imo=8806747

haha Nimbin looks a bit like Amsterdam gone wild...

As for this:

I love beer, so I would like to visit some factories, I like adventures, historical places, big cities, beautiful paths, remote places...

You are describing much of Europe. Is this your first visit?

So before anyone can help you much, please tell us how many nights you will have, and which cities you will enter and depart Europe. It will save you a lot of time and money if you can avoid backtracking — for example, fly in from Brasil to Amsterdam and out to Brasil from Frankfurt.

Also, please let us know what research you have already done so far so that we don't waste time telling you stuff that you already know.

• https://www.lonelyplanet.com/western-europe
• https://wikitravel.org/en/Europe

Thank you Cecilia. For Inter-City Hourly trains, do I need to buy tickets in advance? I arrive in Amsterdam on a Tuesday morning and want to take the train to Brussels three days later on a Friday. Do I need to buy the tickets now (in April) or wait until I get to Amsterdam this summer and buy train tickets a few days before?

You say 'drive' but I assume you are using public transport in and around Leiden? Having a car in western Netherlands is not always practical... high parking fees and lots of traffic jams.

There are direct trains from Schiphol airport to Leiden, probably only takes about 15 minutes. (See that www.ns.nl/en website.)
As said earlier, you don't need to set everything in stone right now. You can visit Amsterdam two days in a row ,or on day 3 and 5 like you say now... but it really doesn't matter. Let the weather be a deciding factor as well... for example Keukenhof is a lot more beautiful if the sun shines and probably not much fun if it rains. Check weather forecasts every day and for the next day. Also install the apps Buienalarm, and Buienradar, they predict rain for the next 2 hours on a very local basis and it's quite accurate. This helps you know when to take shelter in a nice cafe or a museum, or when it's safe to stroll past beautiful canals in any of the cities you want to visit. :-)

Personally I really dislike Brussels. I think Ghent and Bruges are much nicer (could be visited from Rotterdam), or Antwerp which is even closer to Rotterdam.
I also heard Liege is nice (though in a rough, industrial way), this is not so far from Maastricht.
In Aachen don't miss the impressive cathedral.

And like I said earlier I think it's easier to find guided tours once you are in Delft or in The Hague. Not all the way from Leiden. But then again there might be tours that offer a combination, I don't know... ask the Leiden VVV tourist info bureau. There might be private tour operators offering this but it will be a lot more expensive than simply visiting those cities independently (which is perfectly doable and easy).
Our biggest city Amsterdam does not even have a million inhabitants (but 863,000). I think in the eyes of most foreigners, we only have a lot of 'villages'. :-)

My tips for Amsterdam are here: https://obertop.wordpress.com/travel-tips/amsterdam-tips/
If you want to visit Anne Frank House, or Van Gogh Museum (which has a David Hockney combi display this spring), get tickets in advance. I believe for Anne Frank tickets come out about 2 months in advance, and if it seems sold out for your dates, keep trying. They release more tickets in small batches over time, sometimes even on the same day of visiting.
Other museums are fine without advance tickets. Rijksmuseum may have a short line but doable. The cloakroom can get a long line; use a locker instead (if you don't want to carry your coat and bag into the museum). The lockers require a 0.50 or 1 euro coin (not sure which). Rijksmuseum's shop has some surprisingly nice items for sale. The museum itself is huge (plenty for 4 hours or more) so choose which parts you want to see, if you go there.

Great work - it is always a shame with cities like Amsterdam where the same attractions are visited by absolutely everybody. We are heading back in October so we will definitely check some of your ideas out!