Note that I can't directly compare the two since I haven't been to Dubai, but I have been to Berlin and am moving there soon, also for work, and I've researched the Berlin side of things extensively.
As far as the offer goes, I would argue for, in order, 1) more holiday; 2) slightly more pay (maybe 2k Euros per year); 3) more on the relocation if it is a lump sum; 4) more for educational budget. For a senior position, the salary is decent (from my understanding at or above market rate) but the vacation is slightly low (only 4 days above the statutory minimum). On the relocation negotiation, if they don't offer a lump sum, it's probably not worth to negotiate unless you have a lot of things to move. I've never heard of a company offering a flight back every year so it's unlikely it would be offered directly.
As far as saving and money, you can realistically find an apartment by yourself in a nicer part of town for no more than €900-1000 warm per month, but you can definitely save money if you live with a flatmate, live further away, or get a smaller flat. After taxes you'd probably take home about €3000, which means if you had the more lavish flat, you would have €2000 for food, transit, etc. My understanding is that Berlin is relatively cheap for food, so you would struggle to spend more than €500-600 per month even if you ate out often, and you would of course spend less if you cooked your own food. Being conservative and saying you spend €1000 per month on all of your expenditures, you could look at saving, minimum, €1000 per month. If you live frugally you could definitely save more, but with a €5000 per month salary it's going to be impossible to save €4000 per month due to taxes. If saving significantly is very important to you, it would be really bothersome for you.
As far as comparing living in the two places, a lot of other commenters have mentioned about residency, in that if you're university educated, you can get the Blue Card and get permanent residency within 3 years. If you don't have a degree, I think you can get it in 5 (possibly expedited if you can speak German well). Berlin is also quite diverse for Germany, and likely has more job opportunities than Dubai as it doesn't stick to large corporations and the financial sector, especially if you already have experience in Berlin as they won't have to deal with the documents for visa purposes and you would have a better understanding of "how German companies work". The job security in Germany is very high, insofar that it's really difficult to get fired after the initial six months of your contract, but you must also give 3 months notice to your company when you want to leave. Berlin is also quite easy to travel from and to in Europe, via train, bus, and flight, although I understand that Dubai is easy to travel around central Asia and western Europe, so it might be a wash, and maybe a negative in your case since you'll likely be flying further to go back home. Berlin likely has a lot more meetups and networking, and you can use your education budget for conference(s) for networking as well.
Overall, the offer sounds decent (better if you can negotiate), and if you find Berlin more appealing than Dubai I would go for the offer and the opportunity to move. Just keep in mind your priorities (seems the bigger ones are saving and residency, but there must be others you didn't mention) when making the decision, since you are content at your current job and it would be a big move.