I have question regarding the pull-up resistors when UART/I2C lines are running on 2.5V and GND. Is it OK if pull up resistors are used on these lines which are connected to 3.3V or Vice versa when bus is on 3.3V and pull-ups are connected to 2.5V.
Bus on 2.5V, pulling up to 3.3V: It depends on the IC's communicating this bus. When their SDA/SDC input voltages are allowed to become 3.3V, you can pull the lines up to 3.3V. (e.g. some 3.3V uP allow for even 5V input signals). (Do check max input voltage level as well as max input current.)
Bus on 3.3V, pulling up to 2.5V: Check again the datasheets of the IC's communicating this bus how their logic levels are defined.