The pullups on the Wemos board are on pins that have a dedicated bootup function, vaguely similar to the 10k pullup than an AVR Arduino has on RESET. They're not needed, or useful, on an AVR arduino because the way the bootloader works is differently. (pulling GPIO0 low during reset causes the chip to boot from either onboard flash or SD card, depending on GPIO2. Having both pins high at reset (as cause the by pullups) makes the chip boot from internal flash.)
I don't see why you think the ~50k internal pullups are "not very useful", nor why 10-12k would be "more useful", nor how the pullups (r10 and r11, right?) on the Wemos board can be 'combined"...
Are you talking specifically about using pins for I2C? The AVR Arduinos have hardware I2C support, but those pins can't have pullups by default because they're also analog inputs...