There are not a lot of ultra-longhaul flights from Bali (plenty of direct flights to regional hubs around SE Asia). The only nonstop from Bali to Europe that I know of is Turkish Airlines to Istanbul. Although I like Turkish airlines pretty well, honestly, I wouldn't let the hunt for a nonstop to begin this journey exclude other options. Though it's probably as good a way to get to Europe from Bali as any other.
If you live in Bali, you're probably used to very long flights, so getting from place to place within Europe will seem like very short hops.
To the OP's question, I'd offer a few suggestions, one already hinted at...
Mitigating summer heat: Sequence things to minimize extreme heat (start in the far south and work your way north as you get deeper into the full summer season). Of all the places you mention, Malta is going to be the hottest, so I would begin there, work your way north, do Italy from south-to-north, hop over to Croatia, Istanbul or Portugal, finish in Prague/Amsterdam. That way, when July hits, you're in the relatively cool north. That said, if you live in Bali, you're probably used to heat more than many of us on this forum, and you may just shrug off the July heat in Malta (where I would be whining and miserable - I was there in late September/early October and it was plenty hot enough for me).
Of course, whenever going from place to place, it makes sense to choose some kind of logical connection, rather than connecting dots completely at random. Some of your destinations would hint at more/less obvious connections, but a lot of them are going to just be a short, cheap flight, so there's not a major benefit since you can fly pretty easily between most of your list. Malta and Italy are well connected (there are ferries). So are Italy/Croatia. Prague/Amsterdam would be easy by train. For the others, you are probably just looking at short flights.
The other option for sequencing is what I call "a dramatic curve." Some would scoff at the idea, but I often think of a trip as if it were a film, a play or other performance: there are going to be emotional ups and downs, some quiet interludes, dramatic surprises, etc. I like to "finish big" and save some of the real gob-smacking, jaw-dropping stuff for the end of the trip. If you start off with the biggest, most exciting place, it might be all downhill from there. Of course, this depends on whether you're the type to eat dessert first, or save the treats for after dinner.
My spouse generally allows me to do most of the planning for our trips; often she may not know a whole lot about the places we are going, trusting me to plan things for us. I often try to save some surprises for the last parts of the trip, so they help us stay motivated even if we've been traveling for weeks (and starting to run out of energy). The "big finish" tends to cement good memories of the entire trip. But it depends on personality types and of course, what your itinerary options are.
